5Z0B | pdb_00005z0b

Crystal structure of plasma-derived human serum albumin

PDB DOI: https://doi.org/10.2210/pdb5Z0B/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2017-12-19 Released: 2018-12-19
Deposition Author(s): Park, J., Kim, M.-S., Shin, D.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.183 (Depositor), 0.180 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

The crystal structure of plasma-derived human serum albumin

Park, J., Kim, M.S., Shin, D.H.

To be published.

Macromolecule Content

Total Structure Weight: 207.98 kDa
Atom Count: 14,517
Modeled Residue Count: 1,694
Deposited Residue Count: 1,755
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A, B, C	585	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768 Go to UniProtKB: P02768
PHAROS: P02768 GTEx: ENSG00000163631
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02768
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EIC (Subject of Investigation/LOI) Query on EIC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain TA [auth C] SDF format, chain W [auth B] MOL2 format, chain D [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain W [auth B] mmCIF format, chain D [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain W [auth B]	D [auth A], TA [auth C], W [auth B]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain D [auth A] Focus chain TA [auth C] Focus chain W [auth B] Interactions & Density Focus chain D [auth A] Focus chain TA [auth C] Focus chain W [auth B]
PLM (Subject of Investigation/LOI) Query on PLM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain VA [auth C] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain F [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	F [auth A], VA [auth C], Y [auth B], Z [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain VA [auth C] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain F [auth A] Focus chain VA [auth C] Focus chain Y [auth B] Focus chain Z [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain RA [auth B] MOL2 format, chain RA [auth B] mmCIF format, chain RA [auth B]	RA [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain RA [auth B] Interactions & Density Focus chain RA [auth B]
TRP (Subject of Investigation/LOI) Query on TRP Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain H [auth A] SDF format, chain XA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain XA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain XA [auth C]	AA [auth B], H [auth A], XA [auth C]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain AA [auth B] Focus chain H [auth A] Focus chain XA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain H [auth A] Focus chain XA [auth C]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain EB [auth C] SDF format, chain GB [auth C] SDF format, chain NA [auth B] SDF format, chain S [auth A] SDF format, chain U [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A]	EB [auth C], GB [auth C], NA [auth B], S [auth A], U [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain EB [auth C] Focus chain GB [auth C] Focus chain NA [auth B] Focus chain S [auth A] Focus chain U [auth A] Interactions & Density Focus chain EB [auth C] Focus chain GB [auth C] Focus chain NA [auth B] Focus chain S [auth A] Focus chain U [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain KA [auth B] SDF format, chain R [auth A] SDF format, chain SA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth B]	DB [auth C], KA [auth B], R [auth A], SA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DB [auth C] Focus chain KA [auth B] Focus chain R [auth A] Focus chain SA [auth B] Interactions & Density Focus chain DB [auth C] Focus chain KA [auth B] Focus chain R [auth A] Focus chain SA [auth B]
OCA (Subject of Investigation/LOI) Query on OCA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain UA [auth C] SDF format, chain WA [auth C] SDF format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B]	E [auth A], G [auth A], UA [auth C], WA [auth C], X [auth B]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain UA [auth C] Focus chain WA [auth C] Focus chain X [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain UA [auth C] Focus chain WA [auth C] Focus chain X [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain FB [auth C] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain T [auth A] SDF format, chain V [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A]	CB [auth C] FB [auth C] HB [auth C] IA [auth B] JA [auth B] CB [auth C], FB [auth C], HB [auth C], IA [auth B], JA [auth B], LA [auth B], MA [auth B], OA [auth B], PA [auth B], Q [auth A], QA [auth B], T [auth A], V [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CB [auth C] Focus chain FB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain T [auth A] Focus chain V [auth A] Interactions & Density Focus chain CB [auth C] Focus chain FB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain T [auth A] Focus chain V [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	AB [auth C] BA [auth B] BB [auth C] CA [auth B] DA [auth B] AB [auth C], BA [auth B], BB [auth C], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], YA [auth C], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain YA [auth C] Focus chain ZA [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B, C	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.183 (Depositor), 0.180 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.576	α = 90
b = 113.466	β = 104.878
c = 86.809	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Park, J.

Kim, M.-S.

Shin, D.H.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2015R1D1A1A01058942

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 2.0: 2020-06-24
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-10-23
Changes: Structure summary