1VGK | pdb_00001vgk

The crystal structure of class I Major histocompatibility complex, H-2Kd at 2.0 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VGK/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-04-27 Released: 2005-06-28
Deposition Author(s): Zhou, M., Xu, Y., Liu, Y., Gao, G.F., Tien, P., Rao, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of class I major histocompatibility complex, H-2Kd at 2.0 A resolution

Zhou, M., Xu, Y., Liu, Y., Gao, G.F., Tien, P., Rao, Z.

To be published.

Macromolecule Content

Total Structure Weight: 44.73 kDa
Atom Count: 3,583
Modeled Residue Count: 382
Deposited Residue Count: 382
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-D alpha chain	A	274	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01902 (Mus musculus) Explore P01902 Go to UniProtKB: P01902
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01902
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
syvntnmgl	C	9	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.082	α = 90
b = 110.389	β = 90
c = 47.015	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-06-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-06-28
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references
Version 1.4: 2024-11-13
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.