6LF9 | pdb_00006lf9

Crystal structure of pSLA-1*1301 complex with dodecapeptide RVEDVTNTAEYW

PDB DOI: https://doi.org/10.2210/pdb6LF9/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Sus scrofa, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-30 Released: 2021-03-17
Deposition Author(s): Wei, X.H., Wang, S., Zhang, N.Z., Xia, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.291 (Depositor), 0.291 (DCC)
R-Value Work:
0.251 (Depositor), 0.249 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6LF9

This is version 1.3 of the entry. See complete history.

Literature

Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length.

Wei, X.H., Wang, S., Zhang, N.Z., Xia, C.

(2022) Front Immunol

DOI: https://doi.org/10.3389/fimmu.2022.820881

Macromolecule Content

Total Structure Weight: 176.49 kDa
Atom Count: 12,718
Modeled Residue Count: 1,528
Deposited Residue Count: 1,528
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A [auth D], D [auth A], G, J	273	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for B1PJU7 (Sus scrofa) Explore B1PJU7 Go to UniProtKB: B1PJU7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1PJU7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B [auth E], E [auth B], H, K	97	Sus scrofa	Mutation(s): 0 Gene Names: B2M
UniProt
Find proteins for Q07717 (Sus scrofa) Explore Q07717 Go to UniProtKB: Q07717
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07717
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP	C [auth F], F [auth C], I, L	12	synthetic construct	Mutation(s): 0
UniProt
Find proteins for P16082 (Equine infectious anemia virus (strain WSU5)) Explore P16082 Go to UniProtKB: P16082
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16082
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.291 (Depositor), 0.291 (DCC)
R-Value Work: 0.251 (Depositor), 0.249 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.169	α = 90
b = 44.24	β = 90.03
c = 199.631	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2022-03-23
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-11-20
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.