SMTL ID : 7klc.1

Crystal structure of M4H2K1 Fab bound to HIV-1 BG505 gp120 core and to 17b Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.30 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: K.54 Chain E: N.127, T.129, P.131, S.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.54 NAG-NAG.4: 4 residues within 4Å: Chain E: N.155, S.338, N.339 Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: G.26, I.27, T.28 Chain E: R.242, K.243, N.247 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 13 residues within 4Å: Chain E: V.101, S.102, E.104, P.105, K.145, V.147, N.155, N.269, G.271, C.336, V.337, S.338 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.271

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 3 residues within 4Å: Chain E: N.278, S.280 Ligands: NAG.10 No protein-ligand interaction detected (PLIP)

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

NAG.6: 1 residues within 4Å: Chain E: N.45 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.45 NAG.7: 4 residues within 4Å: Chain A: N.57 Chain E: N.169, T.171, N.172 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.172, A:N.57 NAG.8: 5 residues within 4Å: Chain E: Q.186, N.188, R.335, V.337 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.335 NAG.9: 6 residues within 4Å: Chain E: N.188, T.190, H.222, N.224, T.306 Ligands: NAG.8 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.222 NAG.10: 6 residues within 4Å: Chain E: N.255, S.256, S.257, R.360 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.256 NAG.11: 1 residues within 4Å: Chain E: N.231 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.231 NAG.12: 4 residues within 4Å: Chain A: H.61 Chain E: G.349, T.352, N.353 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles. Mbio (2021)

Release Date

2021-07-07

Peptides

M4H2K1 Fab heavy chain: A
M4H2K1 Fab light chain: B
17b Fab light chain: C
17b Fab heavy chain: D
HIV-1 clade A BG505 gp120,HIV-1 clade A BG505 gp120: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

D
D

E
A

M4H2K1 Fab heavy chain

M4H2K1 Fab light chain

17b Fab light chain

17b Fab heavy chain

HIV-1 clade A BG505 gp120,HIV-1 clade A BG505 gp120

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