SMTL ID : 6fr4.1

003 TCR Study of CDR Loop Flexibility

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

hetero-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: Y.121, Q.122, P.200, S.201, P.202 Chain B: S.131, E.132, A.133 Ligands: EDO.8 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.131, B:S.131, B:E.132, B:A.133, A:Q.122 Water bridges: A:Q.122, A:Q.122 GOL.2: 8 residues within 4Å: Chain A: P.15, E.16, K.110, P.111, N.112, S.141, Q.142 Ligands: ACT.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.16, A:K.110, A:K.110 GOL.3: 4 residues within 4Å: Chain A: A.185, F.199 Ligands: EDO.6, EDO.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.197, A:F.199 GOL.13: 6 residues within 4Å: Chain A: S.126, S.128 Chain B: A.126, V.127, A.237, E.238 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:S.126, A:S.128, B:V.127, B:V.127, B:E.238 Water bridges: A:S.126, B:V.127, B:S.236, B:S.236, B:E.238, B:E.238 GOL.14: 5 residues within 4Å: Chain A: M.166 Chain B: Q.139, S.197, A.198, T.199 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.198, B:T.199, B:T.199, B:T.199 GOL.15: 7 residues within 4Å: Chain B: Y.50, Q.55, K.58, G.63, F.65, S.66, G.67 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.50, B:Q.55, B:F.65, B:G.67, B:G.67

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

EDO.4: 1 residues within 4Å: Chain A: D.130 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: T.6, Q.7, I.8, N.23, C.24, S.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.6, A:I.8 Water bridges: A:C.24, A:C.24 EDO.6: 7 residues within 4Å: Chain A: A.185, F.188, N.189, S.191, I.193, F.199 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.185 Water bridges: A:F.188, A:N.189, A:S.191, A:I.193 EDO.7: 6 residues within 4Å: Chain A: S.66, L.67, D.68, R.73, S.74, T.75 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.66, A:T.75, A:T.75 Water bridges: A:D.68 EDO.8: 8 residues within 4Å: Chain A: V.120, Q.122, C.184, A.185, F.199, P.200 Ligands: GOL.1, GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.120 Water bridges: A:A.185 EDO.9: 3 residues within 4Å: Chain A: R.73, T.75, Y.77 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.23, A:R.73 EDO.10: 2 residues within 4Å: Chain A: N.64, Y.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.64 EDO.11: 5 residues within 4Å: Chain A: S.47, L.48, L.49, L.50 Chain B: P.102 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:H.104, A:L.50 Hydrogen bonds: A:L.49 EDO.16: 5 residues within 4Å: Chain B: R.10, Y.11, N.107, G.108, R.110 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.10, B:R.110 Water bridges: B:Y.11, B:R.110, A:G.42, A:G.42, A:G.42 EDO.17: 6 residues within 4Å: Chain B: Q.38, T.39, P.40, A.88, L.89, R.110 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.89, B:R.110, B:R.110 Water bridges: B:Q.38, B:T.39 EDO.18: 7 residues within 4Å: Chain B: E.132, I.135, W.201, Q.202, R.242, A.243, D.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.202, B:D.244, B:D.244 EDO.19: 3 residues within 4Å: Chain B: F.200, N.203, N.206 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.203, B:N.206, B:N.206 EDO.20: 5 residues within 4Å: Chain B: T.114, E.115, K.119, F.151, D.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.114, B:E.115 Water bridges: B:E.115 EDO.21: 4 residues within 4Å: Chain B: E.219, N.220, D.221, E.222 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.219 EDO.22: 5 residues within 4Å: Chain B: R.31, S.52, E.53, S.71, S.73 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.31, B:E.53, B:S.73 Water bridges: B:S.52, B:S.73

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 7 residues within 4Å: Chain A: P.111, N.112, I.113, D.140, S.141, Q.142 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.113, A:D.140 Hydrogen bonds: A:N.112, A:I.113, A:S.141, A:Q.142

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

TCR 003 alpha chain: A
TCR 003 Beta Chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TCR 003 alpha chain

TCR 003 Beta Chain

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