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SMTL ID : 7sif.1

Crystal Structure of HLA B*3505 in complex with NPDIVIYQY, an 9-mer epitope from HIV-I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASN- PRO- ASP- ILE- VAL- ILE- TYR- GLN- TYR: Reverse transcriptase peptide NPDIVIYQY(Non-covalent)

ASN-PRO-ASP-ILE-VAL-ILE-TYR-GLN-TYR.1:

33 residues within 4Å:

Chain A: M.5, Y.7, Y.9, Y.59, R.62, N.63, I.66, F.67, T.69, N.70, T.73, Y.74, E.76, S.77, N.80, L.81, Y.84, L.95, S.97, Y.99, S.116, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, L.156, Y.159, W.167, Y.171
Ligands: BTB.5

35 PLIP interactions:

35 interactions with chain A

Hydrophobic interactions: A:F.67, A:F.67, A:T.69, A:T.73, A:E.76, A:L.81, A:L.95, A:L.95, A:Y.123, A:A.150, A:V.152, A:V.152, A:L.156, A:Y.159, A:W.167
Hydrogen bonds: A:R.62, A:R.62, A:N.63, A:Y.74, A:E.76, A:S.77, A:N.80, A:Y.84, A:S.97, A:Y.99, A:S.116, A:S.116, A:Q.155, A:Q.155, A:Y.171, A:Y.171
Water bridges: A:Y.99, A:Y.99
Salt bridges: A:K.146
pi-Stacking: A:W.147

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2:	4 residues within 4Å: Chain A: T.45, P.47, E.53, W.60 No protein-ligand interaction detected (PLIP)
PEG.3:	5 residues within 4Å: Chain A: A.211, P.235, F.241 Chain B: Y.26, Y.63 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4:

6 residues within 4Å:

Chain A: S.92, H.93, D.119
Chain B: I.1, Q.2, P.32

3 PLIP interactions:

2 interactions with chain A, 1 interactions with chain B

Hydrogen bonds: A:H.93, B:Q.2
Water bridges: A:Q.87

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.5:

16 residues within 4Å:

Chain A: Y.9, N.70, T.73, Y.74, S.97, Y.99, D.114, S.116, W.147, V.152, L.156
Ligands: ASN-PRO-ASP-ILE-VAL-ILE-TYR-GLN-TYR.1, ASN-PRO-ASP-ILE-VAL-ILE-TYR-GLN-TYR.1, ASN-PRO-ASP-ILE-VAL-ILE-TYR-GLN-TYR.1, ASN-PRO-ASP-ILE-VAL-ILE-TYR-GLN-TYR.1, ASN-PRO-ASP-ILE-VAL-ILE-TYR-GLN-TYR.1

6 PLIP interactions:

6 interactions with chain A

Hydrogen bonds: A:N.70, A:S.97, A:D.114, A:S.116
Water bridges: A:Y.99
Salt bridges: A:D.114

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Lobos, C.A. et al., Molecular insights into the HLA-B35 molecules' classification associated with HIV control. Immunol.Cell.Biol. (2024)

Release Date

2022-11-23

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

MHC class I antigen

Beta-2-microglobulin

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