1KPU | pdb_00001kpu

High resolution crystal structure of the MHC class I complex H-2Kb/VSV8

PDB DOI: https://doi.org/10.2210/pdb1KPU/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Vesicular stomatitis Indiana virus
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2002-01-02 Released: 2003-06-10
Deposition Author(s): Rudolph, M.G., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.208 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.194 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

High Resolution Crystal Structure of H-2Kb/VSV8

Rudolph, M.G., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 45.34 kDa
Atom Count: 3,640
Modeled Residue Count: 381
Deposited Residue Count: 381
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A	274	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901 Go to UniProtKB: P01901
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01901
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: P01901-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-2-microglobulin	B	99	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887 Go to UniProtKB: P01887
IMPC: MGI:88127
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
nucleocapsid	C [auth P]	8	N/A	Mutation(s): 0
UniProt
Find proteins for Q88992 (Vesicular stomatitis Indiana virus) Explore Q88992 Go to UniProtKB: Q88992
Entity Groups
UniProt Group	Q88992
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	3		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 2 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] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.208 (Depositor), 0.220 (DCC)
R-Value Work: 0.184 (Depositor), 0.194 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.086	α = 90
b = 88.121	β = 90
c = 45.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-06-10

Deposition Author(s):

Rudolph, M.G.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2003-06-10
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary