SMTL ID : 6oz3.1

Crystal structure of broadly neutralizing antibody N49P9.1 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 8 residues within 4Å: Chain A: N.120, T.122, G.123, I.158, S.160, L.163, H.222 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 NAG.2: 3 residues within 4Å: Chain A: N.115, K.126, N.127 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.126 NAG.3: 7 residues within 4Å: Chain A: P.98, V.140, N.148, N.246, C.308, V.309, S.310 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.140 Hydrogen bonds: A:K.138, A:N.148 NAG.4: 7 residues within 4Å: Chain A: E.161, N.162, T.164 Chain C: H.24, I.25, Y.85 Ligands: NAG.1 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.85, A:N.162, A:T.164 NAG.5: 5 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, K.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.156, A:N.175 NAG.6: 6 residues within 4Å: Chain A: E.179, N.181, T.183, Y.200, K.305, N.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.181, A:Y.200, A:Y.200, A:K.305 NAG.7: 1 residues within 4Å: Chain A: N.204 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: T.241, N.255, T.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.257 NAG.9: 3 residues within 4Å: Chain A: N.261, T.263, C.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.263, A:T.263, A:C.273 NAG.10: 2 residues within 4Å: Chain A: S.177, N.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.177 NAG.11: 1 residues within 4Å: Chain A: N.225 No protein-ligand interaction detected (PLIP)

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

NA.12: 1 residues within 4Å: Chain B: H.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.1, B:H.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Crystal structure of broadly neutralizing antibody N49P9.1 Fab in complex with HIV-1 Clade A/E strain 93TH)57 gp120 core. To Be Published

Release Date

2020-08-19

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
N49P9.1 antibody Fab heavy chain: B
N49P9.1 antibody Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

N49P9.1 antibody Fab heavy chain

N49P9.1 antibody Fab light chain

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