1YB5 | pdb_00001yb5

Crystal structure of human Zeta-Crystallin with bound NADP

PDB DOI: https://doi.org/10.2210/pdb1YB5/pdb

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

Deposited: 2004-12-20 Released: 2004-12-28
Deposition Author(s): Debreczeni, J., Berridge, G., Kavanagh, K., Colbrook, S., Bray, J., Williams, L., Oppermann, U., Sundstrom, M., Arrowsmith, C., Edwards, A., Gileadi, O., von Delft, F., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.207 (Depositor)
R-Value Work:
0.170 (Depositor), 0.168 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of human Zeta-Crystallin at 1.85A

Debreczeni, J., Berridge, G., Kavanagh, K., Colbrook, S., Bray, J., Williams, L., Oppermann, U., Sundstrom, M., Arrowsmith, C., Edwards, A., Gileadi, O., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 77.79 kDa
Atom Count: 5,763
Modeled Residue Count: 648
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Quinone oxidoreductase	A, B	351	Homo sapiens	Mutation(s): 0 Gene Names: CRYZ EC: 1.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q08257 (Homo sapiens) Explore Q08257 Go to UniProtKB: Q08257
PHAROS: Q08257 GTEx: ENSG00000116791
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08257
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B]	G [auth A], N [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B]	H [auth A], I [auth A], J [auth A], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	C [auth A], D [auth A], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	E [auth A], F [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.207 (Depositor)
R-Value Work: 0.170 (Depositor), 0.168 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.484	α = 90
b = 110.239	β = 90
c = 77.253	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-12-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2004-12-28
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: 2024-02-14
Changes: Data collection, Database references, Derived calculations