SMTL ID : 5t6l.2 (1 other biounit)

Crystal structure of 10E8 Fab in complex with the MPER epitope scaffold T117v2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: N.31, W.33, G.53, P.54, G.55, E.56, K.103 Chain C: S.72, G.112, W.114 Ligands: GOL.7 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:W.114, A:N.31, A:G.55, A:E.56, A:K.103 Water bridges: C:S.72, C:G.112 GOL.2: 4 residues within 4Å: Chain A: R.19, S.73, Y.82, E.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.19, A:S.73 GOL.3: 4 residues within 4Å: Chain A: Y.104, Y.105 Chain C: H.69, W.114 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:H.69, A:Y.105 Water bridges: A:K.103, A:F.107 GOL.4: 7 residues within 4Å: Chain A: V.5, E.6, S.7, S.21, C.22, S.23, F.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.5, A:S.7, A:S.23 Water bridges: A:S.23, A:S.23 GOL.5: 6 residues within 4Å: Chain A: G.42, K.43, G.44 Chain B: E.84, Y.86, G.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.86 Water bridges: B:Y.86 GOL.6: 5 residues within 4Å: Chain A: S.7, G.8, R.19, L.20, S.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.7, A:S.21, A:S.21 Water bridges: A:R.19, A:R.19 GOL.7: 6 residues within 4Å: Chain A: K.103 Chain C: D.71, S.72, W.114, I.117 Ligands: GOL.1 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.71, C:S.72, C:S.72, C:S.72 Water bridges: A:K.103, A:K.103 GOL.8: 2 residues within 4Å: Chain B: A.65, S.66 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.65, B:G.67 GOL.9: 7 residues within 4Å: Chain B: L.27, R.28, S.29, H.30, Y.31, A.65, S.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.30, B:A.65 Water bridges: B:G.67, B:G.67 GOL.10: 5 residues within 4Å: Chain A: P.112 Chain B: G.94, R.96 Chain C: F.115, N.119 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.119, B:G.94, B:R.96, B:R.96 GOL.11: 3 residues within 4Å: Chain C: R.14, H.15, D.142 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.15, C:H.15, C:D.142 Water bridges: C:R.14, C:R.14, C:R.14, C:H.15 GOL.12: 7 residues within 4Å: Chain A: G.55 Chain C: V.75, R.76, Q.77, N.78, G.112, N.113 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:G.55, C:R.76, C:N.78, C:N.78 Water bridges: A:G.55, C:S.72, C:V.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Irimia, A. et al., Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design. PLoS Pathog. (2017)

Release Date

2017-03-08

Peptides

Antibody 10E8 FAB HEAVY CHAIN: A
Antibody 10E8 FAB LIGHT CHAIN: B
10E8 EPITOPE SCAFFOLD T117V2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

Antibody 10E8 FAB HEAVY CHAIN

Antibody 10E8 FAB LIGHT CHAIN

10E8 EPITOPE SCAFFOLD T117V2

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