1KPV
High resolution crystal structure of the MHC class I complex H-2Kb/SEV9
- PDB DOI: https://doi.org/10.2210/pdb1KPV/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus, Sendai virus (strain Enders)
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2002-01-02 Released: 2003-06-10 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.204 
- R-Value Work: 0.187 
- R-Value Observed: 0.188 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
H-2 class I histocompatibility antigen, K-B alpha chain | 274 | Mus musculus | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01901 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
beta-2-microglobulin | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01887 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Nucleocapsid protein | C [auth P] | 9 | N/A | Mutation(s): 0  | |
UniProt | |||||
Find proteins for P04857 (Sendai virus (strain Enders)) Explore P04857  Go to UniProtKB:  P04857 | |||||
Entity Groups   | |||||
UniProt Group | P04857 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D 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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MPD Query on MPD | G [auth A], H [auth B], I [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N | |||
PO4 Query on PO4 | E [auth A], F [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.204 
- R-Value Work: 0.187 
- R-Value Observed: 0.188 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 136.287 | α = 90 |
b = 88.342 | β = 90 |
c = 45.322 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
SCALEPACK | data scaling |
CNS | refinement |
DENZO | data reduction |
CNS | phasing |
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