SMTL ID : 9mko.1

4D4 TCR bound to R-phycoerythrin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-1-1-mer

Ligands

24 x PEB: PHYCOERYTHROBILIN(Non-covalent)

PEB.1: 26 residues within 4Å: Chain A: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, C.109, Y.117, L.120, L.122, P.123, S.126, Y.127 Chain D: S.57, I.60, I.67, Y.74, T.75, N.76, M.79 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.66, A:A.72, A:K.78, A:K.81, A:Y.89, A:Y.127 Hydrogen bonds: A:K.78, A:R.84, A:D.85 Salt bridges: A:K.78, A:K.81, A:K.81, A:R.84 pi-Cation interactions: A:R.84 PEB.2: 11 residues within 4Å: Chain A: K.43, L.44, N.47, A.50, V.51, E.54, R.137, C.139, R.142, D.143, F.152 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.43, A:F.152 Hydrogen bonds: A:R.137, A:D.143, A:D.143 Salt bridges: A:R.142 PEB.4: 18 residues within 4Å: Chain B: M.59, N.72, C.73, R.78, A.81, C.82, R.84, D.85, I.88, I.89, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, T.127 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.81, B:I.88, B:I.89, B:L.113, B:Y.117, B:V.122, B:V.122, B:P.123, B:T.127 Hydrogen bonds: B:N.72, B:D.85, B:Y.117, B:Y.117 Salt bridges: B:R.78, B:R.84 PEB.5: 15 residues within 4Å: Chain A: Q.147 Chain B: N.35, K.36, L.38, D.39, I.142, T.153, A.154, D.155, G.156, D.157, C.158, L.161 Chain K: L.24, Q.28 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain K Hydrophobic interactions: B:N.35, B:K.36, B:K.36, B:K.36, B:L.38, B:L.38, B:D.39, B:L.161, K:L.24 Hydrogen bonds: B:N.35, B:D.39, B:G.156 PEB.6: 20 residues within 4Å: Chain B: Y.74, T.75, N.76, M.79 Chain C: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, Y.127 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.66, C:A.72, C:K.78, C:K.81, C:Y.89, C:Y.117, C:L.120, C:L.122, C:L.122, C:Y.127 Hydrogen bonds: C:R.84, C:D.85, C:D.85 Salt bridges: C:K.78, C:K.81, C:R.84 pi-Cation interactions: C:R.84 PEB.7: 12 residues within 4Å: Chain C: K.43, L.44, N.47, V.51, D.136, R.137, L.138, C.139, R.142, D.143, M.144, F.152 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.44, C:L.44, C:L.138, C:F.152 Hydrogen bonds: C:K.43, C:K.43, C:R.142, C:D.143 Salt bridges: C:R.137, C:R.142 PEB.9: 19 residues within 4Å: Chain D: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, I.89, C.109, L.113, Y.117, L.120, V.122, S.126, T.127 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:R.78, D:R.78, D:A.81, D:D.85, D:I.89, D:L.113, D:L.120, D:V.122, D:T.127 Hydrogen bonds: D:N.72, D:N.72, D:R.84, D:D.85, D:D.85 Salt bridges: D:R.77, D:R.84 pi-Cation interactions: D:R.84 PEB.10: 15 residues within 4Å: Chain C: Q.147 Chain D: N.35, K.36, L.38, D.39, A.40, S.43, I.142, N.144, T.153, A.154, G.156, C.158 Chain E: L.24, Q.28 13 PLIP interactions: 10 interactions with chain D, 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:L.38, D:L.38, D:N.144, D:T.153, E:L.24 Hydrogen bonds: D:N.35, D:D.39, D:A.154, D:G.156, E:Q.28, C:Q.147 PEB.11: 23 residues within 4Å: Chain E: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, P.123, S.126, Y.127 Chain H: I.67, Y.74, T.75, N.76, M.79 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:L.66, E:K.81, E:K.81, E:Y.89, E:L.120, E:P.123, E:Y.127 Hydrogen bonds: E:A.72, E:R.84, E:D.85 Salt bridges: E:K.81, E:R.84 PEB.12: 13 residues within 4Å: Chain E: L.44, N.47, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144, F.152 Chain M: T.26 10 PLIP interactions: 1 interactions with chain M, 9 interactions with chain E Hydrogen bonds: M:T.26, E:N.47, E:R.142, E:D.143, E:D.143 Hydrophobic interactions: E:L.44, E:V.51, E:F.152 Salt bridges: E:R.142, E:R.142 PEB.14: 19 residues within 4Å: Chain F: N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, I.89, Y.92, R.108, C.109, L.113, Y.117, L.120, V.122, S.126, T.127 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:A.81, F:D.85, F:I.89, F:Y.92, F:Y.117, F:L.120, F:T.127 Hydrogen bonds: F:R.78, F:D.85, F:D.85, F:Y.117 Salt bridges: F:R.77, F:R.84 PEB.15: 15 residues within 4Å: Chain C: L.24, Q.28 Chain E: R.33, Q.147 Chain F: N.35, K.36, L.38, D.39, A.40, I.142, T.153, A.154, D.155, G.156, C.158 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:K.36, F:L.38, F:D.39 Hydrogen bonds: F:N.35, F:K.36, F:D.39, F:T.153, F:A.154 PEB.16: 13 residues within 4Å: Chain G: K.43, L.44, N.47, A.50, V.51, E.54, T.134, D.136, R.137, C.139, R.142, M.144, F.152 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:L.44, G:T.134, G:R.142, G:F.152 Hydrogen bonds: G:N.47, G:E.54, G:R.137 PEB.17: 20 residues within 4Å: Chain F: I.67, Y.74, T.75, N.76, M.79 Chain G: F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, W.108, C.109, L.120, L.122, P.123, Y.127 17 PLIP interactions: 13 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:A.72, G:K.78, G:K.81, G:L.122, G:Y.127, F:I.67, F:Y.74, F:M.79 Hydrogen bonds: G:K.78, G:R.84, G:D.85, G:D.85, G:H.88, F:S.57 Salt bridges: G:K.78, G:K.81, G:R.84 PEB.18: 19 residues within 4Å: Chain H: M.59, L.66, N.72, C.73, R.78, A.81, C.82, R.84, D.85, I.88, I.89, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:D.85, H:I.88, H:I.89, H:L.113, H:L.113, H:Y.117, H:L.120, H:T.127 Hydrogen bonds: H:N.72, H:N.72, H:N.72, H:Y.117 Salt bridges: H:R.84 PEB.19: 16 residues within 4Å: Chain G: R.33, Q.147 Chain H: N.35, K.36, L.38, D.39, I.142, N.144, T.153, A.154, D.155, G.156, D.157, C.158 Chain I: L.24, Q.28 12 PLIP interactions: 10 interactions with chain H, 1 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: H:K.36, H:L.38, H:L.38, H:N.144, H:T.153, I:L.24 Hydrogen bonds: H:N.35, H:D.39, H:D.39, H:G.156, H:G.156, G:Q.147 PEB.21: 21 residues within 4Å: Chain I: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, W.108, L.120, L.122, P.123, S.126, Y.127 Chain L: I.67, Y.74, T.75, N.76, M.79 15 PLIP interactions: 14 interactions with chain I, 1 interactions with chain L Hydrophobic interactions: I:L.66, I:A.72, I:K.78, I:K.81, I:L.120, I:L.122, I:Y.127, L:Y.74 Hydrogen bonds: I:K.78, I:R.84, I:D.85 Salt bridges: I:K.78, I:K.81, I:R.84 pi-Cation interactions: I:R.84 PEB.22: 15 residues within 4Å: Chain I: K.43, L.44, N.47, A.50, V.51, E.54, T.134, D.136, R.137, L.138, C.139, R.142, D.143, M.144, F.152 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:L.44, I:V.51, I:E.54, I:T.134, I:L.138, I:L.138 Hydrogen bonds: I:K.43, I:N.47, I:R.137 Salt bridges: I:R.137 pi-Cation interactions: I:R.137 PEB.24: 21 residues within 4Å: Chain J: M.59, L.66, N.72, C.73, R.78, A.81, C.82, R.84, D.85, I.88, I.89, Y.92, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:I.88, J:I.89, J:Y.92, J:L.113, J:L.113, J:L.120, J:V.122, J:T.127 Hydrogen bonds: J:N.72, J:N.72, J:N.72, J:Y.117 Salt bridges: J:R.78, J:R.84 PEB.25: 15 residues within 4Å: Chain G: L.24, E.25, Q.28 Chain I: R.33, Q.147 Chain J: N.35, K.36, L.38, D.39, T.153, A.154, D.155, G.156, C.158, L.161 10 PLIP interactions: 2 interactions with chain I, 7 interactions with chain J, 1 interactions with chain G Hydrophobic interactions: I:R.33, J:N.35, J:K.36, J:L.38, J:D.39, J:L.161, G:L.24 Hydrogen bonds: I:Q.147, J:N.35, J:A.154 PEB.26: 22 residues within 4Å: Chain J: Y.74, T.75, N.76 Chain K: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, C.109, Y.117, L.120, L.122, P.123, S.126, Y.127 16 PLIP interactions: 16 interactions with chain K Hydrophobic interactions: K:A.72, K:K.78, K:K.81, K:Y.89, K:L.122, K:L.122, K:L.122, K:Y.127, K:Y.127 Hydrogen bonds: K:R.84, K:R.84, K:D.85, K:Y.127 Salt bridges: K:K.81, K:R.84 pi-Cation interactions: K:R.84 PEB.27: 14 residues within 4Å: Chain K: K.43, L.44, N.47, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144, F.152 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:K.43, K:L.44, K:A.50, K:V.51, K:T.134, K:R.137, K:L.138, K:L.138 Hydrogen bonds: K:D.143 Salt bridges: K:R.137, K:R.142 PEB.29: 20 residues within 4Å: Chain L: M.59, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 19 PLIP interactions: 19 interactions with chain L Hydrophobic interactions: L:A.81, L:Y.92, L:L.113, L:L.113, L:Y.117, L:L.120, L:V.122, L:P.123, L:T.127, L:A.130 Hydrogen bonds: L:N.72, L:R.84, L:D.85, L:D.85, L:Y.117, L:Y.117 Salt bridges: L:R.77, L:R.78, L:R.84 PEB.30: 13 residues within 4Å: Chain A: L.24, Q.28 Chain K: Q.147 Chain L: N.35, K.36, L.38, D.39, I.142, T.153, A.154, D.155, G.156, C.158 12 PLIP interactions: 11 interactions with chain L, 1 interactions with chain A Hydrophobic interactions: L:K.36, L:L.38, L:L.38, L:T.153, L:A.154, A:L.24 Hydrogen bonds: L:N.35, L:D.39, L:D.39, L:A.154, L:G.156, L:G.156

6 x PUB: PHYCOUROBILIN(Non-covalent)

PUB.3: 16 residues within 4Å: Chain B: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, S.136, S.137, A.140, F.141, A.146, S.147, Q.148, R.149 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.140, B:F.141, B:A.146, B:Q.148, B:Q.148 Hydrogen bonds: B:R.129, B:S.137, B:S.147, B:Q.148 PUB.8: 18 residues within 4Å: Chain D: C.50, D.54, S.57, G.58, C.61, E.62, R.129, S.132, I.133, S.136, S.137, A.140, F.141, T.145, A.146, S.147, Q.148, R.149 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.133, D:I.133, D:A.140, D:F.141, D:A.146, D:Q.148, D:R.149 Hydrogen bonds: D:D.54, D:S.132, D:S.147, D:Q.148 Salt bridges: D:R.129 PUB.13: 14 residues within 4Å: Chain F: C.50, D.54, G.58, C.61, E.62, R.129, S.132, I.133, S.136, S.137, A.140, A.146, S.147, Q.148 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:I.133, F:I.133, F:A.146, F:Q.148 Hydrogen bonds: F:D.54, F:E.62, F:E.62, F:S.132, F:S.136, F:S.147, F:Q.148 Salt bridges: F:R.129 PUB.20: 14 residues within 4Å: Chain H: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, S.136, S.137, A.140, F.141, A.146, Q.148 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:D.54, H:I.133, H:F.141, H:A.146 Hydrogen bonds: H:D.54, H:D.54, H:S.136 Salt bridges: H:R.129 PUB.23: 12 residues within 4Å: Chain J: C.50, D.54, S.57, G.58, C.61, R.129, S.132, I.133, S.136, S.137, A.140, F.141 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:I.133, J:I.133, J:A.140 Hydrogen bonds: J:D.54, J:S.136, J:S.136 Salt bridges: J:R.129 PUB.28: 16 residues within 4Å: Chain L: C.50, D.54, S.57, G.58, C.61, R.129, S.132, I.133, S.136, S.137, A.140, F.141, A.146, S.147, Q.148, R.149 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:D.54, L:I.133, L:A.140, L:F.141 Hydrogen bonds: L:D.54, L:D.54, L:S.132, L:S.147, L:Q.148, L:R.149 Salt bridges: L:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rashleigh, L. et al., Antibody-like recognition of a gamma delta T cell receptor toward a foreign antigen. Structure (2025)

Release Date

2025-08-06

Peptides

R-phycoerythrin class I alpha subunit: ACEGIK
R-phycoerythrin class I beta subunit: BDFHJL
4D4 TCR alpha chain: M
4D4 TCR beta chain: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
F

G
I

I
L

K
O

B
B

D
D

F
G

H
J

J
M

L
Q

M
a

N
b

R-phycoerythrin class I alpha subunit

R-phycoerythrin class I beta subunit

4D4 TCR alpha chain

4D4 TCR beta chain

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