SMTL ID : 8vq8.1

Immune receptor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: E.42, G.43, P.44, Q.45 Chain B: F.104 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.43, A:P.44 Water bridges: B:F.104 EDO.2: 4 residues within 4Å: Chain A: D.164, R.166, D.169, K.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.169, A:D.169 EDO.3: 5 residues within 4Å: Chain A: V.87, S.105, G.106 Chain B: Q.41, K.42 No protein-ligand interaction detected (PLIP) EDO.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain B: T.101, Y.103 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.103 Water bridges: A:L.46 EDO.6: 7 residues within 4Å: Chain B: R.51, S.52, P.53, D.73 Chain C: A.66, K.69, H.70 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.66, C:H.70, B:R.51 EDO.7: 4 residues within 4Å: Chain B: T.2, L.3, L.4, F.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.1, B:L.3, B:L.4, B:L.4 EDO.8: 5 residues within 4Å: Chain C: F.110, D.112, N.142, H.148 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain C: D.112, N.142, R.143, D.144 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.112, C:R.143, C:D.144 Water bridges: C:S.146 EDO.10: 4 residues within 4Å: Chain C: W.170, G.171, L.172, E.173 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain C: T.9, E.27 Chain D: M.42, E.44, Y.46 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.46 EDO.12: 5 residues within 4Å: Chain C: Y.15, D.20, L.38, I.65, K.69 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.15, C:K.69 Water bridges: C:D.20, C:G.22, B:S.52 EDO.13: 2 residues within 4Å: Chain C: N.86, W.170 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.86 EDO.14: 8 residues within 4Å: Chain C: V.14, Y.15, Q.16, I.21, G.22, Q.23, P.117, F.139 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.16, C:I.21, C:P.117 EDO.16: 6 residues within 4Å: Chain C: H.6 Chain D: S.121, L.122, R.124, Y.154, P.155 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:L.122, D:R.124, C:H.6

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.15: 2 residues within 4Å: Chain D: N.49, Q.52 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J.B. et al., NP-LCK1-1TCR-MHC complex. To be published

Release Date

2025-01-29

Peptides

T cell receptor - LCK1-1 TRAV6-5 alpha chain: A
T cell receptor - LCK1-1 TRBV1 Beta chain: B
H-2 class II histocompatibility antigen, A-B alpha chain: C
Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

T cell receptor - LCK1-1 TRAV6-5 alpha chain

T cell receptor - LCK1-1 TRBV1 Beta chain

H-2 class II histocompatibility antigen, A-B alpha chain

Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain

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