SMTL ID : 6myy.1

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

18 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: 4 residues within 4Å: Chain A: E.57, 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.10: 4 residues within 4Å: Chain A: E.270, R.311, N.312, E.315 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: T.274, N.402, T.404 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.207, T.209, F.210, 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: 4 residues within 4Å: Chain D: E.57, 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.24: 4 residues within 4Å: Chain D: E.270, R.311, N.312, E.315 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain D: T.274, N.402, T.404 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain D: N.207, T.209, F.210, 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: 4 residues within 4Å: Chain G: E.57, 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.38: 4 residues within 4Å: Chain G: E.270, R.311, N.312, E.315 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 3 residues within 4Å: Chain G: T.274, N.402, T.404 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 4 residues within 4Å: Chain G: N.207, T.209, F.210, 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: 2 residues within 4Å: Chain A: N.128, Y.145 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 2 residues within 4Å: Chain D: N.128, Y.145 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 2 residues within 4Å: Chain G: N.128, Y.145 No protein-ligand interaction detected (PLIP)

3 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: 4 residues within 4Å: Chain A: R.169, N.174 Chain C: K.19 Chain G: R.285 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.19, C:K.19 NAG-NAG-BMA-MAN-MAN-MAN.18: 4 residues within 4Å: Chain A: R.285 Chain D: R.169, N.174 Chain F: K.19 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.19, F:K.19 NAG-NAG-BMA-MAN-MAN-MAN.32: 4 residues within 4Å: Chain D: R.285 Chain G: R.169, N.174 Chain I: K.19 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:K.19, I:K.19

9 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: 4 residues within 4Å: Chain A: E.53, V.55, N.206, N.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: E.246, I.247, N.266, K.323 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: N.278, T.280, I.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain D: E.53, V.55, N.206, N.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain D: E.246, I.247, N.266, K.323 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 3 residues within 4Å: Chain D: N.278, T.280, I.298 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 4 residues within 4Å: Chain G: E.53, V.55, N.206, N.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 4 residues within 4Å: Chain G: E.246, I.247, N.266, K.323 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 3 residues within 4Å: Chain G: N.278, T.280, 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: 8 residues within 4Å: Chain A: P.183, T.186, N.239, R.281, 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: 8 residues within 4Å: Chain D: P.183, T.186, N.239, R.281, 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: 8 residues within 4Å: Chain G: P.183, T.186, N.239, R.281, N.351, C.405, K.406, S.407 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:C.352, G:K.406

3 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: 4 residues within 4Å: Chain A: T.274, Y.305, N.307, M.375 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 4 residues within 4Å: Chain D: T.274, Y.305, N.307, M.375 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.37: 4 residues within 4Å: Chain G: T.274, Y.305, N.307, M.375 No protein-ligand interaction detected (PLIP)

3 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: 4 residues within 4Å: Chain A: T.346, T.347, N.360, S.362 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.25: 4 residues within 4Å: Chain D: T.346, T.347, N.360, S.362 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.39: 4 residues within 4Å: Chain G: T.346, T.347, N.360, S.362 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:I.369 NAG.45: 3 residues within 4Å: Chain A: N.573, S.575, W.576 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.575, A:S.575 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:I.369 NAG.49: 3 residues within 4Å: Chain D: N.573, S.575, W.576 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.575, D:S.575 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:I.369 NAG.53: 3 residues within 4Å: Chain G: N.573, S.575, W.576 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.575, G:S.575 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: BEH
VRC01GL heavy chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
L

E
C

H
F

C
H

F
D

I
G

426c DS-SOSIP D3

VRC01GL light chain

VRC01GL heavy chain

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