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SMTL ID : 1xr8.1

Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LEU- GLU- LYS- ALA- ARG- GLY- SER- THR- TYR: EBNA-3 nuclear protein(Non-covalent)

LEU-GLU-LYS-ALA-ARG-GLY-SER-THR-TYR.1:

30 residues within 4Å:

Chain A: M.5, Y.7, Y.9, M.45, Y.59, R.62, E.63, I.66, S.67, T.73, Y.74, E.76, S.77, N.80, Y.84, L.95, R.97, Y.99, S.116, Y.123, T.143, K.146, W.147, E.152, Q.155, W.156, Y.159, W.167, Y.171
Ligands: GOL.5

29 PLIP interactions:

29 interactions with chain A

Hydrophobic interactions: A:Y.7, A:Y.59, A:Y.74, A:L.95, A:Y.123, A:W.156, A:Y.159, A:Y.159, A:W.167
Hydrogen bonds: A:Y.9, A:R.62, A:R.62, A:E.63, A:E.63, A:S.77, A:N.80, A:Y.84, A:Y.99, A:S.116, A:S.116, A:K.146, A:K.146, A:E.152, A:Y.171, A:Y.171
Water bridges: A:R.97, A:Q.155
Salt bridges: A:K.146
pi-Stacking: A:W.147

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2:

8 residues within 4Å:

Chain A: E.55, G.56, E.58, Y.59, R.62, L.163, W.167, R.170

5 PLIP interactions:

5 interactions with chain A

Hydrogen bonds: A:E.55, A:G.56, A:Y.59, A:R.170
Water bridges: A:R.62

1 x URE: UREA(Non-functional Binders)

URE.3:

8 residues within 4Å:

Chain A: W.204, L.206, R.234, Q.242
Chain B: Y.10, S.11, P.14, R.97

6 PLIP interactions:

1 interactions with chain A, 5 interactions with chain B

Hydrogen bonds: A:R.234, B:S.11, B:S.11, B:R.97
Water bridges: B:M.99, B:M.99

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4:	6 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: F.56, Y.63 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.29, A:D.30, A:D.30, B:Y.63, B:Y.63
GOL.5:	9 residues within 4Å: Chain A: Y.9, N.70, Y.74, R.97, Y.99, W.156 Ligands: LEU-GLU-LYS-ALA-ARG-GLY-SER-THR-TYR.1, LEU-GLU-LYS-ALA-ARG-GLY-SER-THR-TYR.1, LEU-GLU-LYS-ALA-ARG-GLY-SER-THR-TYR.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.70, A:R.97, A:Y.99 Water bridges: A:R.97

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Roder, G. et al., Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype. Acta Crystallogr.,Sect.D (2006)

Release Date

2005-04-14

Peptides

HLA class I histocompatibility antigen, B-15 alpha chain: 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

HLA class I histocompatibility antigen, B-15 alpha chain

Beta-2-microglobulin

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