SMTL ID : 8c8t.1

cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with bNAbs EPTC112 and 3BNC117

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-2-2-2-mer

Ligands

11 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: 6 residues within 4Å: Chain A: N.115, K.130, Y.132 Chain C: D.72, T.73, E.74 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.72, C:T.73 NAG-NAG.3: 3 residues within 4Å: Chain D: Q.260, N.262, R.409 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: N.268, V.407 Chain F: W.103 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:W.103 NAG-NAG.5: 5 residues within 4Å: Chain D: T.264, H.296, N.298, T.380, R.409 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.329, S.330 Ligands: NAG-NAG.7, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: N.352, S.354 Ligands: NAG-NAG.6, NAG-NAG.6, NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain D: N.243 Chain K: G.27, Y.28, Y.67, Y.87 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain E: N.329, S.330, T.338, S.354 Ligands: NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.352, S.354 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain E: E.178, N.229, N.343, G.345, V.411, S.412 Ligands: NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain E: N.243 Chain L: G.27, Y.28, Y.67, Y.87 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:Y.28

2 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.2: 11 residues within 4Å: Chain A: K.219, V.221, L.228, N.229, N.343, C.344, G.345, C.410, V.411, S.412 Ligands: NAG.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.345 NAG-NAG-BMA.10: 7 residues within 4Å: Chain D: L.228, N.229, N.343, G.345, C.410, V.411 Ligands: NAG.29 No protein-ligand interaction detected (PLIP)

1 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.8: 9 residues within 4Å: Chain D: N.115, K.130, Y.132 Chain F: F.53, D.72, T.73, E.74, R.75, F.79 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.72, F:D.72, F:T.73, F:R.75, F:R.75

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

NAG.15: 3 residues within 4Å: Chain A: E.54, N.55 Chain B: S.9 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.100, R.110 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain A: Q.97, S.117, F.118, N.119, K.128, K.130 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: V.141, R.159, N.164, T.165 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: N.262, N.298, V.299, S.300, R.409 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: T.264, H.296, N.298, S.378, T.380, R.409 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: N.329, S.330, T.338, S.354 Ligands: NAG.22 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.352 Ligands: NAG.21 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.268, I.289 Chain C: S.101, W.103 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: P.258, V.411, N.413 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.100, N.103 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain D: T.95, Q.97, S.117, F.118, N.119 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain D: V.141, R.159, N.164, T.165 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.305 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain D: N.229, P.258, N.413 Ligands: NAG-NAG-BMA.10 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.358 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: E.54, N.55 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain E: Q.97, S.117, F.118, N.119, K.130 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: R.159, N.164, T.165 Chain J: W.76 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain E: Q.260, N.262, N.298, R.409 Ligands: NAG.37 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain E: N.229, P.258, N.413 Ligands: NAG-NAG.13 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain E: N.115 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain E: T.264, H.296, N.298, S.378, T.380, R.409 Ligands: NAG.34 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain K: R.61, W.63, E.66, N.68 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Molinos-Albert, L.M. et al., Anti-V1/V3-glycan broadly HIV-1 neutralizing antibodies in a post-treatment controller. Cell Host Microbe (2023)

Release Date

2023-07-05

Peptides

Envelope glycoprotein gp160: ADE
Gp41 Bg505 T332n Sosip.664: BGH
IgG EPTC112 Fab fragment heavy chain: CF
IgG 3BNC117 Fab heavy chain: IJ
IgG 3BNC117 Fab Light Chain: KL
IgG EPTC112 Fab Light Chain: MN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
F

E
G

B
B

G
I

H
J

C
C

F
H

I
R

J
S

K
T

L
U

M
D

N
K

Envelope glycoprotein gp160

Gp41 Bg505 T332n Sosip.664

IgG EPTC112 Fab fragment heavy chain

IgG 3BNC117 Fab heavy chain

IgG 3BNC117 Fab Light Chain

IgG EPTC112 Fab Light Chain

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