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SMTL ID : 1xr9.1

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 1.79 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ILE- LEU- GLY- PRO- PRO- GLY- SER- VAL- TYR: Ubiquitin-conjugating enzyme E2 E1(Non-covalent)

ILE-LEU-GLY-PRO-PRO-GLY-SER-VAL-TYR.1:

29 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, L.81, Y.84, L.95, R.97, Y.99, S.116, Y.123, T.143, K.146, W.147, Q.155, W.156, Y.159, W.167, Y.171

35 PLIP interactions:

35 interactions with chain A

Hydrophobic interactions: A:Y.7, A:Y.59, A:E.63, A:I.66, A:Y.74, A:E.76, A:L.81, A:L.95, A:Y.123, A:T.143, A:Q.155, A:W.167
Hydrogen bonds: A:R.62, A:R.62, A:E.63, A:S.77, A:N.80, A:Y.84, A:Y.99, A:S.116, A:S.116, A:Q.155, A:Y.171, A:Y.171
Water bridges: A:Y.7, A:N.70, A:N.70, A:N.70, A:T.73, A:R.97, A:Y.99, A:E.152, A:E.152
Salt bridges: A:K.146
pi-Stacking: A:W.147

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2:	1 residues within 4Å: Chain A: D.39 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.39 Water bridges: A:R.14 Salt bridges: A:R.14
SO4.5:	3 residues within 4Å: Chain B: S.57, K.58 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.57, B:K.58 Water bridges: B:D.59 Salt bridges: B:K.58

1 x URE: UREA(Non-functional Binders)

URE.3:

7 residues within 4Å:

Chain A: W.204, R.234, Q.242
Chain B: Y.10, S.11, H.13, P.14

6 PLIP interactions:

2 interactions with chain A, 4 interactions with chain B

Hydrogen bonds: A:R.234, A:Q.242, B:S.11, B:S.11
Water bridges: B:S.11, B:M.99

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4:

6 residues within 4Å:

Chain A: T.233, P.235, F.241
Chain B: Y.26, Y.63
Ligands: SO4.5

3 PLIP interactions:

2 interactions with chain A, 1 interactions with chain B

Hydrogen bonds: A:T.233
Water bridges: A:D.30, B:Y.63

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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