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), 0.241 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1VGK

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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01902
Sequence Annotations Expand
Reference Sequence

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.240 (Depositor), 0.241 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.