SMTL ID : 6x5b.1

Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-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: 3 residues within 4Å: Chain A: E.88, N.245, N.257 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.88 NAG-NAG.3: 3 residues within 4Å: Chain F: E.88, N.245, N.257 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:E.88 NAG-NAG.5: 3 residues within 4Å: Chain K: E.88, N.245, N.257 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:E.88

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.2: 16 residues within 4Å: Chain A: S.225, E.227, P.228, V.270, L.277, N.278, C.392, G.393, I.450, R.451, G.452, R.455, C.456, S.457, S.458 Ligands: NAG.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.451 NAG-NAG-BMA-MAN-MAN.4: 16 residues within 4Å: Chain F: S.225, E.227, P.228, V.270, L.277, N.278, C.392, G.393, I.450, R.451, G.452, R.455, C.456, S.457, S.458 Ligands: NAG.24 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.451 NAG-NAG-BMA-MAN-MAN.6: 16 residues within 4Å: Chain K: S.225, E.227, P.228, V.270, L.277, N.278, C.392, G.393, I.450, R.451, G.452, R.455, C.456, S.457, S.458 Ligands: NAG.34 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.451

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

NAG.7: 3 residues within 4Å: Chain A: N.292, T.294, D.295 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: E.309, N.311, N.347 Ligand excluded by PLIP NAG.9: 6 residues within 4Å: Chain A: N.311, T.313, N.347, N.424, T.426 Ligands: NAG.13 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.376, H.377, F.405, N.406 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain A: H.377, V.386, T.387, N.400, T.402 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: P.403, N.406 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: Q.423, N.424 Ligands: NAG.9 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: P.98, W.99, N.100 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain F: N.292, T.294, D.295 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain F: E.309, N.311, N.347 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain F: N.311, T.313, N.347, N.424, T.426 Ligands: NAG.23 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain F: N.376, H.377, F.405, N.406 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain F: H.377, V.386, T.387, N.400, T.402 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain F: P.403, N.406 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain F: Q.423, N.424 Ligands: NAG.19 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain F: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain G: P.98, W.99, N.100 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain K: N.292, T.294, D.295 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain K: E.309, N.311, N.347 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain K: N.311, T.313, N.347, N.424, T.426 Ligands: NAG.33 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain K: N.376, H.377, F.405, N.406 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain K: H.377, V.386, T.387, N.400, T.402 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain K: P.403, N.406 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain K: Q.423, N.424 Ligands: NAG.29 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain K: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.6 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain L: P.98, W.99, N.100 Ligand excluded by PLIP

3 x UOV: N-(4'-methyl[1,1'-biphenyl]-4-yl)-1-oxa-7-azaspiro[3.5]nonane-7-carboxamide(Non-covalent)

UOV.16: 16 residues within 4Å: Chain B: F.7, F.11, L.26, T.27, A.30, V.72, Y.75, I.91, I.92 Chain L: E.73, L.76, R.77, Q.80, L.81, G.83, I.84 13 PLIP interactions: 6 interactions with chain L, 7 interactions with chain B Hydrophobic interactions: L:E.73, L:L.76, L:L.76, L:R.77, L:Q.80, L:L.81, B:F.7, B:F.7, B:V.72, B:Y.75, B:Y.75, B:I.92 pi-Stacking: B:F.11 UOV.26: 16 residues within 4Å: Chain B: E.73, L.76, R.77, Q.80, L.81, G.83, I.84 Chain G: F.7, F.11, L.26, T.27, A.30, V.72, Y.75, I.91, I.92 13 PLIP interactions: 7 interactions with chain G, 6 interactions with chain B Hydrophobic interactions: G:F.7, G:F.7, G:V.72, G:Y.75, G:Y.75, G:I.92, B:E.73, B:L.76, B:L.76, B:R.77, B:Q.80, B:L.81 pi-Stacking: G:F.11 UOV.36: 16 residues within 4Å: Chain G: E.73, L.76, R.77, Q.80, L.81, G.83, I.84 Chain L: F.7, F.11, L.26, T.27, A.30, V.72, Y.75, I.91, I.92 13 PLIP interactions: 6 interactions with chain G, 7 interactions with chain L Hydrophobic interactions: G:E.73, G:L.76, G:L.76, G:R.77, G:Q.80, G:L.81, L:F.7, L:F.7, L:V.72, L:Y.75, L:Y.75, L:I.92 pi-Stacking: L:F.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozorowski, G. et al., A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide. Cell Rep (2020)

Release Date

2020-10-21

Peptides

Envelope glycoprotein gp120: AFK
Envelope glycoprotein gp41: BGL
17b Fab light chain: CHM
T-cell surface glycoprotein CD4: DIN
17b Fab heavy chain: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
D

K
J

B
B

G
E

L
K

C
L

H
F

M
M

D
C

I
G

N
N

E
H

J
I

O
O

Envelope glycoprotein gp120

Envelope glycoprotein gp41

17b Fab light chain

T-cell surface glycoprotein CD4

17b Fab heavy chain

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