SMTL ID : 5vxr.1

The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: Y.150, E.153, S.154, V.155, T.170, F.171, P.172, A.173, M.182 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.150, A:Y.150, A:E.153, A:V.155, A:A.173 Water bridges: A:E.153 GOL.2: 4 residues within 4Å: Chain A: Y.99, G.100, S.101 Chain C: L.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.101, C:L.2 Water bridges: A:Y.99 GOL.3: 8 residues within 4Å: Chain A: P.40, S.86, E.87, T.89, T.115, V.116, L.175, Y.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.86, A:T.89 Water bridges: A:T.89 GOL.4: 8 residues within 4Å: Chain A: P.131, S.140, V.141, T.142, T.187 Chain B: T.118, V.119, S.120 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.120, A:T.142, A:T.142 Water bridges: B:S.120 GOL.5: 4 residues within 4Å: Chain A: T.56, Y.57, Y.58, K.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.56, A:K.63 Water bridges: A:Y.58 GOL.6: 9 residues within 4Å: Chain B: L.15, A.84, I.110, K.111, R.112, A.113, K.173, D.174, S.175 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.111, B:S.175, B:S.175, B:S.175 GOL.7: 4 residues within 4Å: Chain B: S.126, L.129, T.130, K.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.130, B:K.187 GOL.8: 8 residues within 4Å: Chain A: K.38, T.91, Y.93 Chain B: Q.42, K.43, P.44, G.45, Q.46 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.38, B:Q.42, B:K.43, B:G.45, B:Q.46, B:Q.46 Water bridges: B:T.89 GOL.9: 7 residues within 4Å: Chain B: K.43, P.44, D.169, Q.170, D.171, S.172 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.171, B:S.172, B:S.172 Water bridges: B:D.169, B:S.172 GOL.10: 3 residues within 4Å: Chain B: T.5, R.24, S.26 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.5, B:T.5, B:R.24 Water bridges: B:T.5, B:T.5, B:S.7 GOL.11: 11 residues within 4Å: Chain B: Q.42, K.43, P.44, A.87, A.88, T.89, K.107, D.169, Q.170, Y.177 Ligands: GOL.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.89, B:K.107, B:Q.170 Water bridges: B:Q.42, B:T.89, B:Y.177, B:Y.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, J. et al., Escape of Hepatitis C Virus from Epitope I Neutralization Increases Sensitivity of Other Neutralization Epitopes. J. Virol. (2018)

Release Date

2018-02-21

Peptides

MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain: A
MAb24 Variable Light Chain,MAb24 Variable Light Chain: B
Virus Envelope Protein 2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain

MAb24 Variable Light Chain,MAb24 Variable Light Chain

Virus Envelope Protein 2

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