SMTL ID : 6fup.1

F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-mer

Ligands

25 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: H.109, K.159 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: Y.36, L.44, Q.45, L.46 Chain B: F.101 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: S.14, E.15, L.111, P.112, N.113 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: N.61 Ligands: GOL.16 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: K.68, K.69, S.70 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: I.114, Q.115, D.168, F.169, K.170 Ligands: EDO.12 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: N.61, K.78, P.79, S.80, H.82 Ligand excluded by PLIP EDO.8: 1 residues within 4Å: Chain A: E.196 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: E.15, G.16, A.17 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: V.121, Q.123, C.185, A.186, F.200, P.201, S.202 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: K.132, S.133, S.178 Chain B: F.124, L.142 Ligands: EDO.25 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: I.114, N.116, P.117, D.118, D.139, F.169, K.170, S.171 Ligands: EDO.6 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: D.98 Chain B: Y.47, F.49, D.53, N.55 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: R.17, S.64, V.65, S.66, S.74, S.76 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: I.81, P.82, E.111 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: P.200, W.236, G.237, R.238 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: D.2, T.4, S.23, Q.24, T.25 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: R.35, D.61, Y.63, N.83, Q.84 Ligand excluded by PLIP EDO.22: 10 residues within 4Å: Chain A: D.97, D.98 Chain B: R.30, Y.32, F.49, S.93, D.94, E.95, S.96, Y.97 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: L.113, N.114, E.218, W.219, T.220 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: G.57, E.58, I.59, S.60, D.61 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: K.132 Chain B: E.120, A.122, L.142, T.144 Ligands: EDO.11 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: K.115, Q.176, L.179, D.181 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: D.29, R.30, E.95 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain B: K.52, Q.68 Ligand excluded by PLIP

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 7 residues within 4Å: Chain A: V.146, Q.148, S.149, Y.155, I.156, T.157, D.158 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.146, A:I.156 Water bridges: B:K.174 PEG.15: 6 residues within 4Å: Chain A: E.64, A.65, E.66, K.68, H.75, T.77 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.64, A:E.66, A:K.68 Water bridges: A:S.73, A:H.75, A:H.75 PEG.29: 7 residues within 4Å: Chain B: N.9, R.106, D.149, H.150, V.151, E.152, Y.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.9, B:N.9, B:D.149, B:V.151

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 8 residues within 4Å: Chain A: K.58, G.59, I.60, N.61, G.62, F.63, E.64 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.58, A:G.59, A:G.59, A:G.62, A:E.64 Water bridges: A:G.62 GOL.30: 3 residues within 4Å: Chain B: P.7, R.8, N.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.8, B:N.9, B:N.9 Water bridges: B:N.9

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

SO4.31: 3 residues within 4Å: Chain B: D.50, V.51, Q.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.50 Water bridges: B:Q.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holland, C.J. et al., In Silicoand Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility. Front Immunol (2018)

Release Date

2018-04-18

Peptides

Human F11 T-cell Receptor alpha Chain: A
Human F11 T-Cell Receptor beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Human F11 T-cell Receptor alpha Chain

Human F11 T-Cell Receptor beta chain

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