SMTL ID : 6vrq.1

Crystal structure of gl12A21 Fab in complex with anti-idiotypic iv12 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: V.2, Y.32, K.98, F.100, M.101, D.107, Y.108 Chain C: Y.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.98, A:D.107 EDO.2: 14 residues within 4Å: Chain A: L.147, F.172, P.173, A.174, V.175, S.183, L.184, S.185 Chain B: Q.160, E.161, S.162, S.176, S.177, T.178 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.162, B:S.176, B:S.176, B:T.178, A:S.185, A:S.185 EDO.10: 9 residues within 4Å: Chain A: P.102, T.103 Chain B: H.91, H.92, S.93, N.94, L.96 Chain C: Y.33, N.52 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.33 Water bridges: C:N.52, A:K.99 EDO.11: 8 residues within 4Å: Chain C: Y.33, H.35, W.50, D.99, D.104, S.106, W.107 Ligands: K.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.35, C:D.99, C:D.99 EDO.16: 9 residues within 4Å: Chain D: Q.37, K.39, K.45, L.47, V.58, P.59, R.61, F.62, E.81 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.39 Water bridges: D:R.61

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

PEG.3: 10 residues within 4Å: Chain A: S.41, G.42, Q.43 Chain B: K.9, V.85, Y.87, A.100, G.101, T.102, K.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.87, B:K.103, B:K.103 PEG.5: 9 residues within 4Å: Chain B: Q.37, L.47, G.57, V.58, P.59, R.61, F.62, E.81, D.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.37, B:G.57, B:E.81 PEG.14: 7 residues within 4Å: Chain C: G.56, G.57, T.58, N.59, Y.60, Q.65 Ligands: CL.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.56, C:T.58 Water bridges: C:Q.65 PEG.15: 7 residues within 4Å: Chain B: S.30, I.31, S.67 Chain C: R.72, D.73, T.74, S.75 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.74 Water bridges: C:T.74, C:T.74, C:T.74

5 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.4: 4 residues within 4Å: Chain B: M.11, S.12, T.13, V.19 No protein-ligand interaction detected (PLIP) K.12: 3 residues within 4Å: Chain C: I.51, T.71, R.72 No protein-ligand interaction detected (PLIP) K.13: 6 residues within 4Å: Chain C: D.99, S.101, D.103, S.106, W.107 Ligands: EDO.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.99, C:D.103, C:S.106, H2O.7 K.17: 2 residues within 4Å: Chain D: I.29, L.91 No protein-ligand interaction detected (PLIP) K.18: 3 residues within 4Å: Chain D: E.183, H.185, R.207 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:R.207

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

CL.6: 3 residues within 4Å: Chain C: H.173 Chain D: T.160, D.163 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain C: H.110, P.111, W.112 Chain D: K.45, L.46 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: S.30, H.92 Chain C: S.55, G.56 Ligands: PEG.14 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain C: S.88 Ligand excluded by PLIP

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

2021-02-17

Peptides

iv12 Fab Heavy Chain: A
iv12 Fab Light Chain: B
gl12A21 Fab Heavy Chain: C
gl12A21 Fab Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
B

iv12 Fab Heavy Chain

iv12 Fab Light Chain

gl12A21 Fab Heavy Chain

gl12A21 Fab Light Chain