SMTL ID : 7sx6.1 (1 other biounit)

Crystal structure of broadly neutralizing antibody N49P9.3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.47 NAG.2: 6 residues within 4Å: Chain A: N.120, T.122, P.124, I.158, L.163, H.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 NAG.3: 3 residues within 4Å: Chain A: H.44, N.115, N.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.44 NAG.4: 8 residues within 4Å: Chain A: P.98, K.138, N.148, N.246, R.248, C.308, V.309, S.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.138, A:R.248, A:S.310 NAG.5: 6 residues within 4Å: Chain A: E.161, N.162 Chain C: H.24, I.25, I.26, Y.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.24, C:I.26 NAG.6: 6 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, K.176, Q.214 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.176 Hydrogen bonds: A:I.156 NAG.7: 6 residues within 4Å: Chain A: N.181, T.183, Y.200, E.202, K.305, N.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.181, A:T.183, A:Y.200, A:K.305 NAG.8: 2 residues within 4Å: Chain A: N.204, K.207 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: T.241, M.242, N.255, T.257 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.241 Hydrogen bonds: A:N.255 NAG.10: 5 residues within 4Å: Chain A: Q.258, N.261, C.264, G.272, C.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.261, A:G.272

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

CL.11: 2 residues within 4Å: Chain A: K.284, Q.285 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Crystal structure of broadly neutralizing antibody N49P9.3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core. To Be Published

Release Date

2022-11-30

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
N49P9.3 ANTIBODY FAB HEAVY CHAIN: B
N49P9.3 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

N49P9.3 ANTIBODY FAB HEAVY CHAIN

N49P9.3 ANTIBODY FAB LIGHT CHAIN

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