SMTL ID : 3ch1.1 (3 other biounits)

Crystal structure of H-2Db in complex with chimeric gp100

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-oligomer

Ligands

1 x GLU- GLY- PRO- ARG- ASN- GLN- ASP- TRP- LEU: nonameric peptide chimeric gp100(Non-covalent)

GLU-GLY-PRO-ARG-ASN-GLN-ASP-TRP-LEU.1: 32 residues within 4Å: Chain A: M.5, Y.7, E.9, Y.59, R.62, E.63, K.66, Q.70, W.73, F.74, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, F.116, Y.123, T.143, K.146, W.147, S.150, G.151, A.152, H.155, Y.156, Y.159, E.163, W.167, Y.171 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:W.73, A:W.73, A:V.76, A:L.81, A:L.95, A:Y.123, A:W.147, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:E.63, A:K.66, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Y.84, A:Q.97, A:Q.97, A:K.146, A:S.150, A:S.150, A:Y.156, A:E.163, A:Y.171, A:Y.171 Water bridges: A:K.146, A:Y.156, A:Y.156 Salt bridges: A:R.62, A:K.66, A:K.146, A:K.146

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: E.166, W.167, R.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.167, A:R.170 GOL.3: 4 residues within 4Å: Chain A: R.6, F.8, Y.27, N.30 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.30, A:N.30 Water bridges: A:R.6, A:Y.27, B:Y.63, B:Y.63 GOL.5: 5 residues within 4Å: Chain B: H.13, P.20, N.21, I.22, E.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.13 GOL.6: 10 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: S.11, H.13, P.14, P.15, R.97, M.99 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.234, A:Q.242, A:Q.242, B:S.11, B:R.97, B:M.99 GOL.7: 3 residues within 4Å: Chain B: K.41, N.42, K.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.41, B:N.42 GOL.8: 4 residues within 4Å: Chain A: R.121 Chain B: I.1, Q.2, K.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.121, B:Q.2, B:K.3 GOL.9: 2 residues within 4Å: Chain B: I.1, Q.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.2

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

SO4.4: 5 residues within 4Å: Chain A: P.15, G.16, L.17, A.89, G.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:L.17, A:G.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Stipdonk, M.J. et al., Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100. Cancer Res. (2009)

Release Date

2009-03-31

Peptides

H-2 class I histocompatibility antigen, D-B alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

H-2 class I histocompatibility antigen, D-B alpha chain

Beta-2-microglobulin

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