SMTL ID : 7jlk.1

Crystal structure of glVRC01 Fab in complex with anti-idiotype iv1 scFv

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

17 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: Y.101, S.106, A.107 Chain D: Y.94 Ligands: CL.37 Ligand excluded by PLIP NA.2: 4 residues within 4Å: Chain A: Q.39, G.44, L.45 Chain D: F.87 Ligand excluded by PLIP NA.6: 7 residues within 4Å: Chain B: I.51, G.56, T.58, M.70, T.71, R.72 Ligands: CL.11 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain B: G.170, V.171, H.172 Chain C: D.163 Ligand excluded by PLIP NA.8: 3 residues within 4Å: Chain B: T.173 Chain C: T.160, E.161 Ligand excluded by PLIP NA.9: 2 residues within 4Å: Chain B: T.227 Chain C: C.210 Ligand excluded by PLIP NA.14: 4 residues within 4Å: Chain C: A.140, K.141, V.142, E.157 Ligand excluded by PLIP NA.15: 3 residues within 4Å: Chain C: E.79, P.80, E.81 Ligand excluded by PLIP NA.16: 1 residues within 4Å: Chain C: F.93 Ligand excluded by PLIP NA.17: 2 residues within 4Å: Chain C: R.18, T.74 Ligand excluded by PLIP NA.18: 3 residues within 4Å: Chain C: P.59, R.61, E.81 Ligand excluded by PLIP NA.19: 3 residues within 4Å: Chain C: T.20, S.22, T.72 Ligand excluded by PLIP NA.20: 5 residues within 4Å: Chain B: Q.39 Chain C: Q.38, V.85, Y.87 Ligands: EDO.32 Ligand excluded by PLIP NA.21: 3 residues within 4Å: Chain B: Q.113 Chain C: Q.42, A.43 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain B: N.52, S.55, G.57 Chain D: N.53, R.54 Ligand excluded by PLIP NA.34: 2 residues within 4Å: Chain D: P.59, D.60 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain D: D.1, V.3, S.26 Ligand excluded by PLIP

14 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: P.58, S.60, A.69, F.70 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: S.71, L.72 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: E.33, W.50, Y.101 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: P.134, S.135, S.138, A.144, A.145 Chain C: F.112 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: G.56, R.72 Ligands: NA.6 Ligand excluded by PLIP CL.22: 7 residues within 4Å: Chain C: W.144, Q.151, S.152, G.153, N.154, S.155, L.175 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain C: S.22, R.24 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: P.175 Chain C: S.158, V.159 Ligands: EDO.31 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain C: P.137, E.139 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain C: L.4, T.5, Q.6, Q.96, G.97 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: Q.8, K.9, F.10 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain A: S.106 Chain D: N.93, Y.94 Ligands: NA.1 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain A: Y.111 Chain D: H.55 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain D: D.17, R.18 Ligand excluded by PLIP

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 4 residues within 4Å: Chain B: T.124, K.125, G.126, S.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.124, B:G.126 PEG.27: 12 residues within 4Å: Chain B: L.149, V.177, S.185, L.186, S.187 Chain C: V.129, Q.156, E.157, S.158, S.172, S.173, T.174 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:Q.156, C:S.158, C:S.172, B:S.187 Water bridges: B:S.187, B:S.187, B:S.187, B:S.187 PEG.28: 11 residues within 4Å: Chain B: C.224 Chain C: P.115, P.116, L.121, Y.182, F.205, N.206, R.207, G.208, E.209, C.210 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.182, C:G.208, C:E.209 PEG.29: 6 residues within 4Å: Chain C: S.65, G.66, S.67, D.70, F.71, T.72 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.65, C:T.72 PEG.30: 9 residues within 4Å: Chain A: T.28, T.30, Y.54 Chain C: S.31, D.50, A.51, S.52, S.65, G.66 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.66, A:T.30 Water bridges: C:G.64

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

EDO.13: 8 residues within 4Å: Chain B: Y.153, E.156, P.157, V.158, F.174, P.175, A.176, L.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.158, B:V.158, B:A.176 EDO.31: 8 residues within 4Å: Chain B: P.175 Chain C: K.99, R.138, V.159, T.160, E.161, Y.169 Ligands: CL.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.138, C:R.138 EDO.32: 8 residues within 4Å: Chain B: Q.39, Y.95 Chain C: Q.38, K.39, P.40, G.41, Q.42 Ligands: NA.20 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.38, C:G.41, C:Q.42, B:Y.95, B:Y.95 EDO.40: 7 residues within 4Å: Chain D: Q.37, K.39, K.45, L.47, V.58, P.59, F.62 3 PLIP interactions: 3 interactions with chain D Water bridges: D:Q.37, D:Q.37, D:A.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seydoux, E. et al., Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies. Cell Rep (2021)

Release Date

2021-03-31

Peptides

iv1 Heavy Chain: A
glVRC01 Heavy Chain: B
glVRC01 Light Chain: C
iv1 Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
A

C
B

D
L

iv1 Heavy Chain

glVRC01 Heavy Chain

glVRC01 Light Chain

iv1 Light Chain

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