SMTL ID : 6mzj.1

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs bound, sharpened map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

21 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: 3 residues within 4Å: Chain A: N.58, G.489, S.490 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: E.246, I.247, N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: R.311, N.312 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain A: N.402 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: N.207, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain A: S.362, G.363, N.366, T.368 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain D: N.58, G.489, S.490 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain D: N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain D: E.246, I.247, N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain D: R.311, N.312 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain D: N.402 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain D: N.207, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain D: S.362, G.363, N.366, T.368 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain G: N.58, G.489, S.490 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain G: N.100 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain G: E.246, I.247, N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 2 residues within 4Å: Chain G: R.311, N.312 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 1 residues within 4Å: Chain G: N.402 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 2 residues within 4Å: Chain G: N.207, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 4 residues within 4Å: Chain G: S.362, G.363, N.366, T.368 No protein-ligand interaction detected (PLIP)

3 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.3: 1 residues within 4Å: Chain A: N.128 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 1 residues within 4Å: Chain D: N.128 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 1 residues within 4Å: Chain G: N.128 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.4: 1 residues within 4Å: Chain A: N.174 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.18: 1 residues within 4Å: Chain D: N.174 No protein-ligand interaction detected (PLIP)

7 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.5: 3 residues within 4Å: Chain A: E.53, N.206, N.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain A: N.278, I.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain D: E.53, N.206, N.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 2 residues within 4Å: Chain D: N.278, I.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 1 residues within 4Å: Chain G: N.174 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 3 residues within 4Å: Chain G: E.53, N.206, N.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 2 residues within 4Å: Chain G: N.278, I.298 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.6: 6 residues within 4Å: Chain A: P.183, N.239, N.351, C.405, K.406, S.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.352, A:K.406 NAG-NAG-BMA-MAN-MAN-MAN-MAN.20: 6 residues within 4Å: Chain D: P.183, N.239, N.351, C.405, K.406, S.407 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.352, D:K.406 NAG-NAG-BMA-MAN-MAN-MAN-MAN.34: 6 residues within 4Å: Chain G: P.183, N.239, N.351, C.405, K.406, S.407 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:C.352, G:K.406

4 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.9: 1 residues within 4Å: Chain A: N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 1 residues within 4Å: Chain D: N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.37: 1 residues within 4Å: Chain G: N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.39: 2 residues within 4Å: Chain G: T.346, N.360 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.11: 2 residues within 4Å: Chain A: T.346, N.360 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.25: 2 residues within 4Å: Chain D: T.346, N.360 No protein-ligand interaction detected (PLIP)

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

NAG.43: 3 residues within 4Å: Chain A: H.330, N.332, N.424 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.424 NAG.44: 4 residues within 4Å: Chain A: S.314, I.369, S.370, N.371 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:S.314 NAG.45: 2 residues within 4Å: Chain A: N.573, S.575 No protein-ligand interaction detected (PLIP) NAG.46: 1 residues within 4Å: Chain A: N.599 No protein-ligand interaction detected (PLIP) NAG.47: 3 residues within 4Å: Chain D: H.330, N.332, N.424 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:N.424 NAG.48: 4 residues within 4Å: Chain D: S.314, I.369, S.370, N.371 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:S.314 NAG.49: 2 residues within 4Å: Chain D: N.573, S.575 No protein-ligand interaction detected (PLIP) NAG.50: 1 residues within 4Å: Chain D: N.599 No protein-ligand interaction detected (PLIP) NAG.51: 3 residues within 4Å: Chain G: H.330, N.332, N.424 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:N.424 NAG.52: 4 residues within 4Å: Chain G: S.314, I.369, S.370, N.371 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:S.314 NAG.53: 2 residues within 4Å: Chain G: N.573, S.575 No protein-ligand interaction detected (PLIP) NAG.54: 1 residues within 4Å: Chain G: N.599 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borst, A.J. et al., Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. Elife (2018)

Release Date

2018-11-14

Peptides

426c DS-SOSIP D3: ADG
VRC01GL light chain: BE
VRC01GL heavy chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
L

E
C

C
H

F
D

426c DS-SOSIP D3

VRC01GL light chain

VRC01GL heavy chain

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