SMTL ID : 9o62.1

1C5H 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(Covalent)(Non-covalent)

PEB.1: 17 residues within 4Å: Chain A: L.24, E.25, Q.28 Chain I: R.33, Q.147 Chain J: N.35, K.36, L.38, D.39, I.142, S.143, N.144, T.153, A.154, A.155, G.156, C.158 14 PLIP interactions: 2 interactions with chain A, 10 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: A:L.24, J:N.35, J:K.36, J:L.38, J:L.38, J:N.144, J:A.154, I:Q.147 Hydrogen bonds: A:Q.28, J:N.35, J:D.39, J:A.154, J:G.156, I:Q.147 PEB.2: 28 residues within 4Å: Chain A: C.59, F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, V.116, Y.117, L.120, L.122, P.123, S.126, Y.127 Chain H: S.57, I.60, I.67, Y.74, T.75, N.76, M.79 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain H Hydrophobic interactions: A:L.66, A:L.66, A:K.78, A:K.81, A:K.81, A:D.85, A:H.88, A:Y.89, A:L.92, A:V.116, A:Y.117, A:L.120, A:L.122, A:Y.127, A:Y.127, H:I.67, H:Y.74 Hydrogen bonds: A:K.78, A:R.84, A:Y.127, H:S.57, H:T.75 Salt bridges: A:K.78, A:K.81, A:R.84 PEB.3: 14 residues within 4Å: Chain A: 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.43, A:A.50, A:V.51, A:R.137, A:L.138, A:F.152 Hydrogen bonds: A:K.43, A:N.47, A:R.142 Salt bridges: A:R.137, A:R.142 pi-Cation interactions: A:R.142 PEB.4: 18 residues within 4Å: Chain A: R.33, Q.147, E.151 Chain B: N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, A.155, G.156, C.158 Chain I: L.24, Q.28 19 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: B:N.35, B:K.36, B:K.36, B:L.38, B:L.38, B:A.40, B:N.144, B:A.154, A:R.33, A:Q.147, I:L.24 Hydrogen bonds: B:N.35, B:D.39, B:D.39, B:T.153, B:A.154, B:G.156, A:Q.147, I:Q.28 PEB.6: 23 residues within 4Å: Chain B: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:Y.92, B:T.116, B:Y.117, B:L.120, B:V.122, B:P.123, B:A.130 Hydrogen bonds: B:N.72, B:R.84, B:Y.117 Salt bridges: B:R.77, B:R.78, B:R.84 pi-Cation interactions: B:R.84 PEB.7: 26 residues within 4Å: Chain C: C.59, F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, Y.117, L.120, L.122, P.123, S.126, Y.127 Chain L: I.60, I.67, Y.74, T.75, N.76, M.79 27 PLIP interactions: 6 interactions with chain L, 21 interactions with chain C Hydrophobic interactions: L:I.60, L:I.67, L:Y.74, L:M.79, C:L.66, C:A.72, C:K.81, C:K.81, C:D.85, C:H.88, C:Y.89, C:L.92, C:L.122, C:L.122, C:P.123, C:Y.127, C:Y.127, C:Y.127 Hydrogen bonds: L:S.57, L:T.75, C:R.84, C:D.85, C:Y.127 Salt bridges: C:K.78, C:K.81, C:R.84 pi-Cation interactions: C:H.88 PEB.8: 13 residues within 4Å: Chain C: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144, F.152 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:K.43, C:L.44, C:A.50, C:V.51, C:L.138, C:R.142, C:D.143, C:F.152 Hydrogen bonds: C:K.43, C:N.47, C:R.142 Salt bridges: C:R.137, C:R.142 pi-Cation interactions: C:R.137 PEB.10: 22 residues within 4Å: Chain D: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:Y.92, D:T.116, D:Y.117, D:L.120, D:V.122, D:T.127, D:A.130 Hydrogen bonds: D:N.72, D:D.85 Salt bridges: D:R.77, D:R.78 PEB.11: 20 residues within 4Å: Chain C: R.33, Q.147, E.151 Chain D: N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, A.155, G.156, C.158 Chain G: S.21, L.24, E.25, Q.28 17 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: D:N.35, D:K.36, D:L.38, D:N.144, D:T.153, D:A.154, C:R.33, C:Q.147, G:L.24, G:L.24 Hydrogen bonds: D:N.35, D:D.39, D:T.153, D:A.154, D:G.156, C:Q.147, G:Q.28 PEB.12: 25 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 J: S.57, I.60, I.67, Y.74, T.75, N.76, M.79 25 PLIP interactions: 20 interactions with chain E, 5 interactions with chain J Hydrophobic interactions: E:L.66, E:A.72, E:K.78, E:K.81, E:K.81, E:H.88, E:Y.89, E:L.122, E:P.123, E:Y.127, E:Y.127, J:I.67, J:Y.74, J:M.79 Hydrogen bonds: E:K.78, E:R.84, E:D.85, E:Y.127, J:S.57, J:T.75 Salt bridges: E:K.78, E:K.81, E:R.84 pi-Cation interactions: E:R.84, E:H.88 PEB.13: 13 residues within 4Å: Chain E: 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 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:K.43, E:A.50, E:V.51, E:R.137, E:L.138, E:R.142, E:R.142 Hydrogen bonds: E:N.47, E:R.137, E:R.137 Salt bridges: E:R.137, E:R.142 pi-Cation interactions: E:R.142 PEB.15: 23 residues within 4Å: Chain F: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:Y.92, F:T.116, F:L.120, F:A.130 Hydrogen bonds: F:N.72, F:D.85 Salt bridges: F:R.77, F:R.78, F:R.84 PEB.16: 20 residues within 4Å: Chain E: R.33, Q.147, V.150, E.151 Chain F: N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, A.155, G.156, C.158 Chain K: L.24, E.25, Q.28 20 PLIP interactions: 13 interactions with chain F, 5 interactions with chain E, 2 interactions with chain K Hydrophobic interactions: F:N.35, F:K.36, F:L.38, F:L.38, F:A.40, F:N.144, F:T.153, F:A.154, E:R.33, E:Q.147, E:V.150, K:L.24 Hydrogen bonds: F:N.35, F:D.39, F:T.153, F:A.154, F:G.156, E:R.33, E:Q.147, K:Q.28 PEB.17: 26 residues within 4Å: Chain B: S.57, I.60, I.67, Y.74, T.75, N.76, M.79 Chain G: C.59, 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 27 PLIP interactions: 6 interactions with chain B, 21 interactions with chain G Hydrophobic interactions: B:I.60, B:I.67, B:Y.74, B:M.79, G:L.66, G:A.72, G:K.78, G:K.81, G:K.81, G:H.88, G:Y.89, G:L.120, G:L.122, G:P.123, G:Y.127, G:Y.127 Hydrogen bonds: B:S.57, B:T.75, G:K.78, G:R.84, G:D.85, G:Y.127 Salt bridges: G:K.78, G:K.81, G:R.84 pi-Cation interactions: G:R.84, G:H.88 PEB.18: 12 residues within 4Å: Chain G: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:K.43, G:A.50, G:V.51, G:R.137, G:L.138 Hydrogen bonds: G:K.43, G:N.47, G:R.137, G:R.137, G:R.142, G:R.142 Salt bridges: G:R.137 pi-Cation interactions: G:R.142 PEB.20: 22 residues within 4Å: Chain H: M.59, L.66, N.72, C.73, R.77, R.78, M.79, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:L.66, H:R.78, H:R.78, H:A.81, H:I.88, H:Y.92, H:L.113, H:Y.117, H:L.120, H:P.123, H:A.130 Hydrogen bonds: H:N.72, H:R.84, H:D.85 Salt bridges: H:R.77, H:R.78, H:R.84 pi-Cation interactions: H:R.84 PEB.21: 18 residues within 4Å: Chain C: L.24, E.25, Q.28 Chain G: R.33, Q.147 Chain H: N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, A.155, G.156, C.158 15 PLIP interactions: 10 interactions with chain H, 3 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: H:N.35, H:K.36, H:K.36, H:L.38, H:L.38, H:N.144, H:A.154, C:L.24, C:Q.28, G:Q.147 Hydrogen bonds: H:N.35, H:D.39, H:G.156, C:Q.28, G:Q.147 PEB.22: 24 residues within 4Å: Chain F: I.60, I.67, Y.74, T.75, N.76, M.79 Chain I: 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 25 PLIP interactions: 20 interactions with chain I, 5 interactions with chain F Hydrophobic interactions: I:L.66, I:K.78, I:K.78, I:H.88, I:Y.89, I:L.120, I:L.122, I:P.123, I:Y.127, I:Y.127, I:Y.127, F:I.60, F:I.67, F:Y.74, F:M.79 Hydrogen bonds: I:K.78, I:R.84, I:D.85, I:Y.127, F:T.75 Salt bridges: I:K.78, I:K.81, I:R.84 pi-Cation interactions: I:R.84, I:H.88 PEB.23: 13 residues within 4Å: Chain I: 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 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:K.43, I:A.50, I:V.51, I:R.137, I:L.138 Hydrogen bonds: I:K.43, I:N.47 Salt bridges: I:R.137, I:R.142 pi-Cation interactions: I:R.142 PEB.25: 23 residues within 4Å: Chain J: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:A.81, J:D.85, J:I.88, J:Y.92, J:T.116, J:L.120, J:A.130 Hydrogen bonds: J:N.72, J:D.85, J:Y.117 Salt bridges: J:R.77, J:R.78, J:R.84 PEB.26: 25 residues within 4Å: Chain D: S.57, I.60, I.67, Y.74, T.75, N.76, M.79 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, Y.117, L.120, L.122, P.123, S.126, Y.127 28 PLIP interactions: 22 interactions with chain K, 6 interactions with chain D Hydrophobic interactions: K:L.66, K:A.72, K:K.78, K:K.81, K:K.81, K:H.88, K:Y.89, K:L.120, K:L.120, K:L.122, K:P.123, K:Y.127, K:Y.127, D:I.60, D:I.67, D:Y.74, D:M.79 Hydrogen bonds: K:K.78, K:R.84, K:D.85, K:Y.127, D:S.57, D:T.75 Salt bridges: K:K.78, K:K.81, K:R.84 pi-Cation interactions: K:R.84, K:H.88 PEB.27: 13 residues within 4Å: Chain K: K.43, L.44, N.47, 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:V.51, K:E.54, K:R.137, K:L.138, K:F.152 Hydrogen bonds: K:K.43, K:N.47 Salt bridges: K:R.137 pi-Cation interactions: K:R.137, K:R.142 PEB.29: 23 residues within 4Å: Chain L: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 16 PLIP interactions: 16 interactions with chain L Hydrophobic interactions: L:R.78, L:A.81, L:I.88, L:Y.92, L:T.116, L:Y.117, L:L.120, L:V.122, L:P.123, L:A.130 Hydrogen bonds: L:N.72, L:D.85 Salt bridges: L:R.77, L:R.78, L:R.84 pi-Cation interactions: L:R.84 PEB.30: 19 residues within 4Å: Chain E: L.24, E.25, Q.28 Chain K: R.33, Q.147, E.151 Chain L: N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, A.155, G.156, C.158 19 PLIP interactions: 13 interactions with chain L, 3 interactions with chain K, 3 interactions with chain E Hydrophobic interactions: L:N.35, L:K.36, L:K.36, L:L.38, L:L.38, L:A.40, L:N.144, L:A.154, K:R.33, K:Q.147, E:L.24, E:L.24 Hydrogen bonds: L:N.35, L:D.39, L:T.153, L:A.154, L:G.156, K:Q.147, E:Q.28

6 x PUB: PHYCOUROBILIN(Non-covalent)(Covalent)

PUB.5: 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, P.147, Q.148, R.149 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.133, B:I.133, B:A.140, B:F.141, B:A.146, B:Q.148 Hydrogen bonds: B:D.54, B:S.136 Salt bridges: B:R.129 PUB.9: 15 residues within 4Å: Chain D: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, S.136, S.137, A.140, A.146, P.147, Q.148, R.149 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:D.54, D:I.133, D:I.133, D:I.133, D:A.146, D:Q.148 Hydrogen bonds: D:D.54, D:S.136, D:Q.148, D:R.149 Salt bridges: D:R.129 PUB.14: 16 residues within 4Å: Chain F: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, S.136, S.137, A.140, A.146, P.147, Q.148, R.149 Chain N: R.100 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:D.54, F:I.133, F:I.133, F:I.133, F:A.146, F:Q.148 Hydrogen bonds: F:D.54, F:S.136, F:Q.148, F:R.149 Salt bridges: F:R.129 PUB.19: 16 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, P.147, Q.148, R.149 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:D.54, H:I.133, H:I.133, H:A.146, H:Q.148 Hydrogen bonds: H:D.54, H:S.136, H:Q.148 Salt bridges: H:R.129 PUB.24: 15 residues within 4Å: Chain J: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, S.136, S.137, A.140, A.146, P.147, Q.148, R.149 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:I.133, J:I.133, J:A.146, J:Q.148, J:R.149 Hydrogen bonds: J:D.54, J:S.136, J:Q.148, J:R.149 Salt bridges: J:R.129 PUB.28: 16 residues within 4Å: Chain L: 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, P.147, Q.148, R.149 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:D.54, L:I.133, L:A.140, L:F.141, L:A.146, L:Q.148 Hydrogen bonds: L:S.136, 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
1C5H TCR delta chain: M
TCR gamma chain: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

B
B

D
D

F
F

H
H

J
J

L
L

M
a

N
b

R-phycoerythrin class I alpha subunit

R-phycoerythrin class I beta subunit

1C5H TCR delta chain

TCR gamma chain

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