SMTL ID : 3cch.6 (5 other biounits)

H-2Db complex with murine gp100

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLU- GLY- SER- ARG- ASN- GLN- ASP- TRP- LEU: nonameric peptide murine gp100(Non-covalent)

GLU-GLY-SER-ARG-ASN-GLN-ASP-TRP-LEU.1: 28 residues within 4Å: Chain A: M.5, Y.7, E.63, K.66, Q.70, W.73, F.74, 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:K.66, A:W.73, A:W.73, A:W.73, A:L.81, A:L.95, A:Y.123, A:T.143, A:W.147, A:W.167 Hydrogen bonds: A:Y.7, A:Y.59, A:E.63, 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:S.99, A:S.99, A:S.150, A:S.150, A:Y.156, A:Y.159, A:Y.171, A:Y.171 Salt bridges: A:K.66, A:K.146, A:K.146 GLU-GLY-SER-ARG-ASN-GLN-ASP-TRP-LEU.8: 29 residues within 4Å: Chain C: M.5, Y.7, 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 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:K.66, C:W.73, C:W.73, C:V.76, C:L.81, C:L.95, C:Y.123, C:T.143, C:W.147, C:W.167 Hydrogen bonds: C:E.63, C:K.66, C:Q.70, C:Q.70, C:S.77, C:N.80, C:Q.97, C:Q.97, C:S.99, C:S.99, C:T.143, C:K.146, C:W.147, C:S.150, C:S.150, C:Y.156, C:Y.156, C:Y.171 Salt bridges: C:K.66, C:K.146, C:K.146

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

SO4.2: 2 residues within 4Å: Chain A: R.111, Y.113 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.111 SO4.4: 2 residues within 4Å: Chain B: K.3, T.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.4, B:T.4 SO4.5: 2 residues within 4Å: Chain B: R.12, H.67 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.12, B:H.67 SO4.6: 8 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: S.11, H.13, P.14, P.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.234, A:Q.242, B:S.11 SO4.7: 4 residues within 4Å: Chain B: I.35, E.36, I.37, M.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.35, B:I.37 SO4.10: 8 residues within 4Å: Chain C: W.204, R.234, Q.242 Chain D: S.11, H.13, P.14, P.15, R.97 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.234, C:Q.242, D:S.11 SO4.11: 2 residues within 4Å: Chain D: K.3, T.4 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.4, D:T.4 SO4.12: 4 residues within 4Å: Chain D: K.41, F.70, T.71, Y.78 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.71, D:Y.78, D:Y.78 Salt bridges: D:K.41 SO4.13: 3 residues within 4Å: Chain D: T.73, W.95, R.97 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.73, D:R.97 Salt bridges: D:R.97

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.8, Y.27, N.30 Chain B: F.56, K.58, Y.63 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.30, B:Y.63, B:Y.63 GOL.9: 5 residues within 4Å: Chain C: R.6, F.8, Y.27, N.30 Chain D: K.58 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.4, C:N.30

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

2009-03-10

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
A

B
H

D
B

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

Beta-2-microglobulin

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