SMTL ID : 3cch.5 (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: 29 residues within 4Å: Chain A: 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 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:K.66, A:W.73, A:W.73, A:V.76, A:L.81, A:L.95, A:Y.123, A:T.143, A:W.147, A:W.167 Hydrogen bonds: A:E.63, A:K.66, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Q.97, A:Q.97, A:S.99, A:S.99, A:T.143, A:K.146, A:W.147, A:S.150, A:S.150, A:Y.156, A:Y.156, A:Y.159, A:Y.171 Salt bridges: A:K.66, A:K.146, A:K.146 GLU-GLY-SER-ARG-ASN-GLN-ASP-TRP-LEU.10: 28 residues within 4Å: Chain C: 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 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:K.66, C:W.73, C:W.73, C:W.73, C:L.81, C:L.95, C:Y.123, C:T.143, C:W.147, C:W.167 Hydrogen bonds: C:Y.7, C:Y.59, C:E.63, C:E.63, C:K.66, C:Q.70, C:Q.70, C:S.77, C:N.80, C:Y.84, C:Q.97, C:Q.97, C:S.99, C:S.99, C:S.150, C:S.150, C:Y.156, C:Y.171, C:Y.171 Salt bridges: C:K.66, C:K.146, C:K.146

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

SO4.2: 5 residues within 4Å: Chain D: K.41, E.69, F.70, T.71, Y.78 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.71 Salt bridges: D:K.41 SO4.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.5: 8 residues within 4Å: Chain A: W.204, R.234, Q.242 Chain B: S.11, H.13, P.14, P.15, R.97 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.11, A:R.234, A:Q.242 SO4.6: 2 residues within 4Å: Chain B: K.3, T.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.4, B:T.4, B:T.4 SO4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.8: 4 residues within 4Å: Chain B: K.41, F.70, T.71, Y.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.71, B:Y.78 Salt bridges: B:K.41 SO4.9: 5 residues within 4Å: Chain B: T.73, D.76, W.95, R.97 Chain C: L.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.74, B:R.97 Salt bridges: B:R.97 SO4.11: 3 residues within 4Å: Chain C: R.21 Chain D: M.54 Ligands: SO4.16 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:R.21 Hydrogen bonds: D:M.54 SO4.12: 1 residues within 4Å: Chain C: Y.113 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.113 Salt bridges: C:R.111 SO4.14: 2 residues within 4Å: Chain D: K.3, T.4 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.4 SO4.15: 2 residues within 4Å: Chain D: R.12, H.67 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.12, D:H.67 SO4.16: 5 residues within 4Å: Chain D: I.35, E.36, I.37, M.51 Ligands: SO4.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.35, D:I.37

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, N.30 Chain B: F.56, K.58 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.56 Water bridges: A:N.30 GOL.13: 5 residues within 4Å: Chain C: F.8, Y.27, N.30 Chain D: F.56, Y.63 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.58, D:Y.63, C:Y.27

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
D

C
J

B
E

D
K

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

Beta-2-microglobulin

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