1Z6Z | pdb_00001z6z

Crystal Structure of Human Sepiapterin Reductase in complex with NADP+

PDB DOI: https://doi.org/10.2210/pdb1Z6Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-03-23 Released: 2005-04-05
Deposition Author(s): Ugochukwu, E., Kavanagh, K., Ng, S., Arrowsmith, C., Edwards, A., Sundstrom, M., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.245 (Depositor), 0.250 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Human Sepiapterin Reductase

Ugochukwu, E., Kavanagh, K., Ng, S., Arrowsmith, C., Edwards, A., Sundstrom, M., von Delft, F., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 188.25 kDa
Atom Count: 12,116
Modeled Residue Count: 1,562
Deposited Residue Count: 1,692
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sepiapterin reductase	A, B, C, D, E A, B, C, D, E, F	282	Homo sapiens	Mutation(s): 0 Gene Names: SPR EC: 1.1.1.153
UniProt & NIH Common Fund Data Resources
Find proteins for P35270 (Homo sapiens) Explore P35270 Go to UniProtKB: P35270
PHAROS: P35270 GTEx: ENSG00000116096
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35270
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain P [auth C] SDF format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain P [auth C] MOL2 format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain P [auth C] mmCIF format, chain J [auth A]	J [auth A] L [auth B] P [auth C] S [auth D] V [auth E] J [auth A], L [auth B], P [auth C], S [auth D], V [auth E], X [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain X [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain I [auth A]	H [auth A] I [auth A] K [auth B] M [auth C] N [auth C] H [auth A], I [auth A], K [auth B], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D], T [auth E], U [auth E], W [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.245 (Depositor), 0.250 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.274	α = 90
b = 95.001	β = 90.57
c = 162.825	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-04-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description