3REZ

glycoprotein GPIb variant

PDB DOI: https://doi.org/10.2210/pdb3REZ/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2011-04-05 Released: 2012-02-15
Deposition Author(s): McEwan, P.A., Yang, W., Carr, K.H., Mo, X., Zheng, X., Li, R., Emsley, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.259
R-Value Work: 0.211
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 58.54 kDa
Atom Count: 3,897
Modelled Residue Count: 455
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX	A, B, C, D	129	Homo sapiens	Mutation(s): 0 Gene Names: GP1BB, GP9
UniProt & NIH Common Fund Data Resources
Find proteins for P14770 (Homo sapiens) Explore P14770 Go to UniProtKB: P14770
PHAROS: P14770 GTEx: ENSG00000169704
Find proteins for P13224 (Homo sapiens) Explore P13224 Go to UniProtKB: P13224
PHAROS: P13224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P14770P13224
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain O [auth D]	E [auth A], G [auth B], J [auth C], L [auth C], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth C] Focus chain O [auth D]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C]	K [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
FUL Query on FUL Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C]	I [auth C]	beta-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-KGJVWPDLSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain R [auth D] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D]	F [auth A] H [auth B] M [auth C] N [auth C] P [auth D] F [auth A], H [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.259
R-Value Work: 0.211
R-Value Observed: 0.214
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.01	α = 90
b = 72.01	β = 90
c = 171.731	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2017-08-23
Changes: Advisory, Refinement description, Source and taxonomy
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

3REZ

glycoprotein GPIb variant

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)