SMTL ID : 9mgb.1

scFv antibody CL33 bound to R-phycoerythrin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-mer

Ligands

24 x PEB: PHYCOERYTHROBILIN(Non-covalent)(Covalent)

PEB.1: 23 residues within 4Å: Chain A: F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, W.108, V.116, Y.117, L.120, L.122, P.123, S.126, Y.127 Chain D: I.60, I.67, Y.74, T.75, N.76, M.79 23 PLIP interactions: 3 interactions with chain D, 20 interactions with chain A Hydrophobic interactions: D:I.67, D:Y.74, D:M.79, A:A.72, A:K.78, A:K.81, A:K.81, A:H.88, A:V.116, A:Y.117, A:L.122, A:L.122, A:Y.127, A:Y.127 Hydrogen bonds: A:K.78, A:R.84, A:D.85, A:D.85, A:Y.127 Salt bridges: A:K.78, A:K.81, A:R.84 pi-Cation interactions: A:R.84 PEB.2: 17 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 Chain N: E.66, S.144, L.238 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain N Hydrophobic interactions: A:A.50, A:V.51, A:R.137, A:L.138, A:F.152, N:L.238 Hydrogen bonds: A:R.137, A:D.143, N:L.238 Salt bridges: A:R.137, A:R.142 pi-Cation interactions: A:R.137 PEB.4: 21 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, I.89, Y.92, R.108, C.109, L.113, Y.117, L.120, V.122, S.126, T.127 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:D.85, B:I.88, B:I.89, B:Y.92, B:L.113, B:L.113, B:V.122, B:T.127 Hydrogen bonds: B:N.72, B:N.72, B:R.77, B:R.78, B:R.84, B:D.85 Salt bridges: B:R.84 pi-Cation interactions: B:R.84 PEB.5: 19 residues within 4Å: Chain A: R.33, Q.147, V.150 Chain B: N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, D.155, G.156, C.158 Chain K: L.24, E.25, Q.28 18 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B, 2 interactions with chain K Hydrophobic interactions: A:R.33, A:Q.147, A:V.150, B:N.35, B:K.36, B:L.38, B:A.40, B:N.144, K:L.24 Hydrogen bonds: A:R.33, B:N.35, B:D.39, B:D.39, B:T.153, B:A.154, B:A.154, B:G.156, K:Q.28 PEB.6: 21 residues within 4Å: Chain B: I.67, 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, W.108, L.120, L.122, P.123, S.126, Y.127 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.72, C:K.78, C:K.81, C:K.81, C:H.88, C:L.120, C:L.122, C:L.122, C:Y.127, C:Y.127, B:I.67, B:Y.74, B:M.79 Hydrogen bonds: C:R.84, C:D.85, C:Y.127 Salt bridges: C:K.78, C:K.81, C:R.84 pi-Cation interactions: C:R.84 PEB.7: 19 residues within 4Å: Chain C: 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 Chain Q: E.66, S.144, K.237, L.238, P.239 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain Q Hydrophobic interactions: C:A.50, C:V.51, C:T.134, C:R.137, C:L.138, C:R.142, C:F.152, Q:L.238 Hydrogen bonds: C:K.43, C:D.143 Salt bridges: C:R.137, C:R.142, Q:K.69 pi-Cation interactions: C:R.137 PEB.9: 24 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, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, T.127, A.130 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:D.85, D:I.88, D:I.89, D:Y.92, D:L.113, D:L.113, D:T.116, D:Y.117, D:L.120, D:L.120, D:V.122, D:V.122, D:P.123, D:T.127, D:A.130 Hydrogen bonds: D:N.72, D:N.72, D:R.84, D:D.85, D:D.85, D:L.120 Salt bridges: D:R.77, D:R.78, D:R.84 pi-Cation interactions: D:R.84 PEB.10: 19 residues within 4Å: Chain C: R.33, Q.147 Chain D: A.32, N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, D.155, G.156, C.158 Chain E: L.24, E.25, Q.28 21 PLIP interactions: 17 interactions with chain D, 2 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: D:N.35, D:K.36, D:K.36, D:L.38, D:L.38, D:A.40, D:N.144, D:A.154, C:Q.147, E:L.24 Hydrogen bonds: D:N.35, D:N.35, D:N.35, D:K.36, D:D.39, D:T.153, D:A.154, D:A.154, D:G.156, C:Q.147, E:Q.28 PEB.11: 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, 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 24 PLIP interactions: 4 interactions with chain H, 20 interactions with chain E Hydrophobic interactions: H:I.67, H:Y.74, H:M.79, E:A.72, E:K.78, E:K.81, E:K.81, E:H.88, E:V.116, E:Y.117, E:L.122, E:L.122, E:Y.127, E:Y.127 Hydrogen bonds: H:S.57, E:K.78, E:R.84, E:D.85, E:D.85, E:Y.127 Salt bridges: E:K.81, E:K.81, E:R.84 pi-Cation interactions: E:R.84 PEB.12: 16 residues within 4Å: Chain E: K.43, L.44, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144, F.152 Chain M: S.144, K.237, L.238 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain M Hydrophobic interactions: E:A.50, E:V.51, E:E.54, E:T.134, E:R.137, E:L.138, E:R.142, M:L.238 Hydrogen bonds: E:K.43, M:L.238 Salt bridges: E:R.137, E:R.142 pi-Cation interactions: E:R.137 PEB.14: 22 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, I.89, Y.92, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:A.81, F:D.85, F:I.88, F:I.89, F:Y.92, F:L.113, F:L.113, F:V.122, F:T.127 Hydrogen bonds: F:N.72, F:N.72, F:N.72, F:D.85 Salt bridges: F:R.77, F:R.78, F:R.84 PEB.15: 19 residues within 4Å: Chain C: L.24, E.25, Q.28 Chain E: R.33, Q.147 Chain F: A.32, N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, D.155, G.156, C.158 21 PLIP interactions: 15 interactions with chain F, 4 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: F:N.35, F:K.36, F:K.36, F:L.38, F:A.40, F:N.144, F:A.154, E:R.33, E:Q.147, C:L.24 Hydrogen bonds: F:N.35, F:K.36, F:D.39, F:D.39, F:T.153, F:A.154, F:A.154, F:G.156, E:R.33, E:Q.147, C:Q.28 PEB.16: 24 residues within 4Å: Chain F: S.57, I.60, 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, V.116, Y.117, L.120, L.122, P.123, S.126, Y.127 22 PLIP interactions: 5 interactions with chain F, 17 interactions with chain G Hydrophobic interactions: F:I.67, F:Y.74, F:M.79, G:A.72, G:K.78, G:K.81, G:H.88, G:V.116, G:Y.117, G:L.120, G:Y.127, G:Y.127 Hydrogen bonds: F:S.57, F:S.57, G:K.78, G:R.84, G:D.85, G:D.85 Salt bridges: G:K.78, G:K.81, G:R.84 pi-Cation interactions: G:R.84 PEB.17: 19 residues within 4Å: Chain G: 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 Chain P: Y.63, S.144, K.237, L.238 16 PLIP interactions: 12 interactions with chain G, 4 interactions with chain P Hydrophobic interactions: G:K.43, G:L.44, G:A.50, G:V.51, G:R.137, G:L.138, G:F.152, P:L.238, P:L.238 Hydrogen bonds: G:N.47, G:D.143, G:D.143, P:L.238 Salt bridges: G:R.137, P:K.237 pi-Cation interactions: G:R.137 PEB.19: 21 residues within 4Å: Chain H: M.59, 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, P.123, S.126, T.127 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:A.81, H:D.85, H:I.88, H:I.89, H:Y.92, H:L.113, H:L.113, H:L.120, H:V.122, H:T.127 Hydrogen bonds: H:N.72, H:N.72, H:N.72, H:D.85 Salt bridges: H:R.77, H:R.78, H:R.84 PEB.20: 19 residues within 4Å: Chain G: R.33, Q.147 Chain H: A.32, N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, D.155, G.156, C.158 Chain I: L.24, E.25, Q.28 20 PLIP interactions: 15 interactions with chain H, 3 interactions with chain G, 2 interactions with chain I Hydrophobic interactions: H:N.35, H:K.36, H:K.36, H:L.38, H:L.38, H:A.40, H:N.144, H:A.154, G:R.33, G:Q.147, I:L.24 Hydrogen bonds: H:N.35, H:K.36, H:D.39, H:T.153, H:A.154, H:A.154, H:G.156, G:Q.147, I:Q.28 PEB.21: 21 residues within 4Å: Chain I: F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, W.108, Y.117, L.120, L.122, P.123, S.126, Y.127 Chain L: I.67, Y.74, T.75, N.76, M.79 22 PLIP interactions: 19 interactions with chain I, 3 interactions with chain L Hydrophobic interactions: I:A.72, I:K.78, I:K.81, I:K.81, I:H.88, I:Y.117, I:L.122, I:L.122, I:Y.127, I:Y.127, L:I.67, L:Y.74, L:M.79 Hydrogen bonds: I:K.78, I:R.84, I:D.85, I:D.85, I:Y.127 Salt bridges: I:K.78, I:K.81, I:R.84 pi-Cation interactions: I:R.84 PEB.22: 13 residues within 4Å: Chain I: K.43, L.44, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, F.152 Chain R: L.238 15 PLIP interactions: 12 interactions with chain I, 3 interactions with chain R Hydrophobic interactions: I:L.44, I:A.50, I:V.51, I:T.134, I:R.137, I:L.138, I:F.152, R:L.238 Hydrogen bonds: I:D.143, R:L.238 Salt bridges: I:K.43, I:R.137, I:R.142, R:K.237 pi-Cation interactions: I:R.137 PEB.24: 20 residues within 4Å: Chain J: M.59, 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, Y.117, L.120, V.122, P.123, S.126, T.127 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:A.81, J:I.88, 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:D.85 Salt bridges: J:R.77, J:R.78, J:R.84 PEB.25: 19 residues within 4Å: Chain G: L.24, E.25, Q.28 Chain I: R.33, Q.147 Chain J: A.32, N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, D.155, G.156, C.158 18 PLIP interactions: 15 interactions with chain J, 1 interactions with chain G, 2 interactions with chain I Hydrophobic interactions: J:N.35, J:K.36, J:K.36, J:L.38, J:L.38, J:A.40, J:N.144, J:A.154, G:L.24, I:Q.147 Hydrogen bonds: J:N.35, J:K.36, J:D.39, J:D.39, J:T.153, J:A.154, J:G.156, I:Q.147 PEB.26: 23 residues within 4Å: Chain J: I.60, I.67, Y.74, T.75, N.76, M.79 Chain K: F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, W.108, V.116, Y.117, L.120, L.122, P.123, S.126, Y.127 23 PLIP interactions: 20 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: K:A.72, K:K.78, K:K.81, K:K.81, K:H.88, K:V.116, K:Y.117, K:L.122, K:L.122, K:Y.127, K:Y.127, J:I.67, J:Y.74, J:M.79 Hydrogen bonds: K:K.78, K:R.84, K:D.85, K:D.85, K:Y.127 Salt bridges: K:K.78, K:K.81, K:R.84 pi-Cation interactions: K:R.84 PEB.27: 15 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 Chain O: L.238 14 PLIP interactions: 13 interactions with chain K, 1 interactions with chain O Hydrophobic interactions: K:A.50, K:V.51, K:E.54, K:T.134, K:R.137, K:L.138, K:F.152, O:L.238 Hydrogen bonds: K:K.43, K:R.142, K:D.143 Salt bridges: K:R.137, K:R.142 pi-Cation interactions: K:R.137 PEB.29: 22 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, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, S.126, T.127 20 PLIP interactions: 20 interactions with chain L Hydrophobic interactions: L:R.78, L:A.81, L:D.85, L:I.88, L:I.89, L:Y.92, L:L.113, L:L.113, L:T.116, L:L.120, L:V.122, L:T.127 Hydrogen bonds: L:N.72, L:N.72, L:R.84, L:D.85 Salt bridges: L:R.77, L:R.78, L:R.84 pi-Cation interactions: L:R.84 PEB.30: 18 residues within 4Å: Chain A: L.24, E.25, Q.28 Chain K: R.33, Q.147 Chain L: N.35, K.36, L.38, D.39, A.40, I.142, S.143, N.144, T.153, A.154, D.155, G.156, C.158 17 PLIP interactions: 14 interactions with chain L, 1 interactions with chain A, 2 interactions with chain K 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, A:L.24, K:Q.147 Hydrogen bonds: L:N.35, L:D.39, L:T.153, L:A.154, L:A.154, L:G.156, K:Q.147

6 x PUB: PHYCOUROBILIN(Non-covalent)

PUB.3: 18 residues within 4Å: Chain B: 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.133, B:I.133, B:A.140, B:F.141, B:F.141, B:Q.148, B:Q.148, B:R.149 Hydrogen bonds: B:D.54, B:S.132, B:S.147, B:Q.148 Salt bridges: B:R.129 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 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.133, D:I.133, D:I.133, D:F.141, D:F.141, D:Q.148, D:R.149 Hydrogen bonds: D:D.54, D:S.132, D:T.145, D:S.147, D:Q.148 Salt bridges: D:R.129 PUB.13: 18 residues within 4Å: Chain F: 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 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:I.133, F:I.133, F:F.141, F:F.141, F:Q.148, F:R.149 Hydrogen bonds: F:D.54, F:T.145, F:S.147, F:Q.148 Salt bridges: F:R.129 PUB.18: 17 residues within 4Å: Chain H: 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, A.146, S.147, Q.148, R.149 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:D.54, H:I.133, H:A.140, H:F.141, H:A.146, H:Q.148, H:R.149 Hydrogen bonds: H:D.54, H:D.54, H:S.132, H:S.136, H:S.147, H:Q.148 Salt bridges: H:R.129 PUB.23: 18 residues within 4Å: Chain J: 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 J Hydrophobic interactions: J:I.133, J:I.133, J:I.133, J:F.141, J:F.141, J:Q.148, J:R.149 Hydrogen bonds: J:D.54, J:S.132, J:S.147, J:Q.148 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, S.147, Q.148, R.149 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:D.54, L:I.133, L:I.133, L:F.141, L:A.146, L:Q.148, L:R.149 Hydrogen bonds: L:D.54, L:S.136, L:S.147, L:Q.148

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 alpha chain: ACEGIK
R-phycoerythrin beta chain: BDFHJL
CL33 scFv: MNOPQR

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
c

O
e

P
g

Q
i

R
k

R-phycoerythrin alpha chain

R-phycoerythrin beta chain

CL33 scFv

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