SMTL ID : 6opq.1

CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

24 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: E.88, V.90, L.91, N.245, N.257 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.90 NAG-NAG.3: 3 residues within 4Å: Chain A: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: E.309, N.311, N.347, S.349, R.455 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: T.313, N.347, N.424, T.426 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: I.374, F.375, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: V.386, T.387, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 8 residues within 4Å: Chain A: P.403, N.406, D.416, P.418, G.420, E.422, N.424, I.425 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.425 Hydrogen bonds: A:G.420 NAG-NAG.9: 6 residues within 4Å: Chain A: N.347, E.422, Q.423, N.424 Ligands: NAG-NAG.4, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain F: E.88, V.90, L.91, N.245, N.257 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.90 NAG-NAG.12: 3 residues within 4Å: Chain F: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain F: E.309, N.311, N.347, S.349, R.455 Ligands: NAG-NAG.18, NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain F: T.313, N.347, N.424, T.426 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain F: I.374, F.375, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain F: V.386, T.387, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 8 residues within 4Å: Chain F: P.403, N.406, D.416, P.418, G.420, E.422, N.424, I.425 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:I.425 Hydrogen bonds: F:G.420 NAG-NAG.18: 6 residues within 4Å: Chain F: N.347, E.422, Q.423, N.424 Ligands: NAG-NAG.13, NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain K: E.88, V.90, L.91, N.245, N.257 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:V.90 NAG-NAG.21: 3 residues within 4Å: Chain K: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 7 residues within 4Å: Chain K: E.309, N.311, N.347, S.349, R.455 Ligands: NAG-NAG.27, NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain K: T.313, N.347, N.424, T.426 Ligands: NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain K: I.374, F.375, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain K: V.386, T.387, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 8 residues within 4Å: Chain K: P.403, N.406, D.416, P.418, G.420, E.422, N.424, I.425 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:I.425 Hydrogen bonds: K:G.420 NAG-NAG.27: 6 residues within 4Å: Chain K: N.347, E.422, Q.423, N.424 Ligands: NAG-NAG.22, NAG-NAG.23 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.2: 16 residues within 4Å: Chain A: V.224, S.225, E.227, P.228, R.268, V.270, L.277, N.278, C.392, G.393, I.450, G.452, Q.453, S.457, S.458 Ligands: NAG.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.452, A:Q.453 NAG-NAG-BMA-MAN-MAN.11: 16 residues within 4Å: Chain F: V.224, S.225, E.227, P.228, R.268, V.270, L.277, N.278, C.392, G.393, I.450, G.452, Q.453, S.457, S.458 Ligands: NAG.33 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.452, F:Q.453 NAG-NAG-BMA-MAN-MAN.20: 16 residues within 4Å: Chain K: V.224, S.225, E.227, P.228, R.268, V.270, L.277, N.278, C.392, G.393, I.450, G.452, Q.453, S.457, S.458 Ligands: NAG.36 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.452, K:Q.453

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

NAG.28: 6 residues within 4Å: Chain A: F.249, N.250, G.251, S.252, G.253, P.254 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.249 NAG.29: 6 residues within 4Å: Chain A: N.354, W.409, R.413, T.414, D.415, D.416 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.409 Hydrogen bonds: A:T.414, A:D.415 NAG.30: 5 residues within 4Å: Chain A: N.278, S.457, S.458, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG.31: 6 residues within 4Å: Chain F: F.249, N.250, G.251, S.252, G.253, P.254 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.249 NAG.32: 6 residues within 4Å: Chain F: N.354, W.409, R.413, T.414, D.415, D.416 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:W.409 Hydrogen bonds: F:T.414, F:D.415 NAG.33: 5 residues within 4Å: Chain F: N.278, S.457, S.458, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG.34: 6 residues within 4Å: Chain K: F.249, N.250, G.251, S.252, G.253, P.254 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:F.249 NAG.35: 6 residues within 4Å: Chain K: N.354, W.409, R.413, T.414, D.415, D.416 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:W.409 Hydrogen bonds: K:T.414, K:D.415 NAG.36: 5 residues within 4Å: Chain K: N.278, S.457, S.458, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.20 No protein-ligand interaction detected (PLIP)

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 gp160: AFK
17b Fab light chain: BGL
Envelope glycoprotein gp41: 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
E

B
L

G
N

L
O

C
B

H
F

M
G

D
C

I
I

N
J

E
H

J
K

O
M

Envelope glycoprotein gp160

17b Fab light chain

Envelope glycoprotein gp41

T-cell surface glycoprotein CD4

17b Fab heavy chain

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