3M0W | pdb_00003m0w

Structure of S100A4 with PCP

PDB DOI: https://doi.org/10.2210/pdb3M0W/pdb

Classification: Calcium Binding Protein
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-03 Released: 2010-05-12
Deposition Author(s): Ramagopal, U.A., Dulyaninova, N.G., Almo, S.C., Bresnick, A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.302 (Depositor), 0.290 (DCC)
R-Value Work:
0.252 (Depositor), 0.250 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of S100A4 with PCP

Ramagopal, U.A., Dulyaninova, N.G., Almo, S.C., Bresnick, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 121.61 kDa
Atom Count: 7,351
Modeled Residue Count: 891
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A4	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	100	Homo sapiens	Mutation(s): 0 Gene Names: CAPL, MTS1, S100A4
UniProt & NIH Common Fund Data Resources
Find proteins for P26447 (Homo sapiens) Explore P26447 Go to UniProtKB: P26447
PHAROS: P26447 GTEx: ENSG00000196154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26447
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P77 Query on P77 Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth I] SDF format, chain LA [auth I] SDF format, chain O [auth B] SDF format, chain OA [auth J] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] EA [auth G] HA [auth H] K [auth A] KA [auth I] BA [auth F], EA [auth G], HA [auth H], K [auth A], KA [auth I], LA [auth I], O [auth B], OA [auth J], R [auth B], S [auth C], V [auth D], Y [auth E]	2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine C₂₀ H₂₄ Cl N₃ S WIKYUJGCLQQFNW-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain R [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain R [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain RA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth J]	N [auth A], RA [auth J]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain RA [auth J] Interactions & Density Focus chain N [auth A] Focus chain RA [auth J]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth I] SDF format, chain NA [auth I] SDF format, chain P [auth B] SDF format, chain PA [auth J] SDF format, chain Q [auth B] SDF format, chain QA [auth J] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain NA [auth I] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain NA [auth I] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth E] CA [auth F] DA [auth F] FA [auth G] GA [auth G] AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], L [auth A], M [auth A], MA [auth I], NA [auth I], P [auth B], PA [auth J], Q [auth B], QA [auth J], T [auth C], U [auth C], W [auth D], X [auth D], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.302 (Depositor), 0.290 (DCC)
R-Value Work: 0.252 (Depositor), 0.250 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.577	α = 90
b = 102.275	β = 92.6
c = 117.37	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description