SMTL ID : 6opp.1

Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

16 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 C: F.249, N.250, S.252, P.254 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain C: E.309, N.311, N.347, I.348, S.349 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain C: T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: V.386, T.387, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.278, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain G: N.250, S.252 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain G: E.88, V.90, N.245, N.257 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:E.88, G:V.90 NAG-NAG.16: 9 residues within 4Å: Chain G: E.309, N.311, N.347, I.348, S.349, R.455 Ligands: NAG-NAG-BMA.21, NAG-NAG-BMA.21, NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 8 residues within 4Å: Chain G: N.311, T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.21, NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain G: V.386, T.387, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain G: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.14, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain L: T.248, F.249, N.250, G.253 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain L: E.88, V.90, N.245, N.257 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:V.90 NAG-NAG.27: 8 residues within 4Å: Chain L: E.309, N.311, N.347, I.348, S.349 Ligands: NAG-NAG-BMA.32, NAG-NAG-BMA.32, NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 7 residues within 4Å: Chain L: N.311, T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.32 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain L: N.278, S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.25, NAG-NAG.27 No protein-ligand interaction detected (PLIP)

10 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: 4 residues within 4Å: Chain C: E.88, V.90, N.245, N.257 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.88, C:V.90 NAG-NAG-BMA.4: 4 residues within 4Å: Chain C: N.292, T.294, D.295 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain C: K.350, P.403, N.406, D.415, N.424 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 7 residues within 4Å: Chain C: N.347, Q.423, N.424 Ligands: NAG-NAG.5, NAG-NAG.5, NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain G: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 6 residues within 4Å: Chain G: K.350, P.403, N.406, Y.417, Q.423, N.424 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:K.350 NAG-NAG-BMA.21: 7 residues within 4Å: Chain G: N.347, Q.423, N.424 Ligands: NAG-NAG.16, NAG-NAG.16, NAG-NAG.17, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 4 residues within 4Å: Chain L: V.386, T.387, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 8 residues within 4Å: Chain L: K.350, P.403, N.406, S.407, D.416, Y.417, N.424, I.425 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:K.350, L:I.425 NAG-NAG-BMA.32: 5 residues within 4Å: Chain L: N.347, Q.423, N.424 Ligands: NAG-NAG.27, NAG-NAG.28 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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.3: 15 residues within 4Å: Chain C: V.224, S.225, E.227, P.228, V.270, L.277, N.278, G.393, I.450, R.451, G.452, R.455, S.457, S.458 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 14 residues within 4Å: Chain G: V.224, S.225, E.227, P.228, L.277, N.278, G.393, I.450, R.451, G.452, Q.453, S.457, S.458 Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP)

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.7: 3 residues within 4Å: Chain C: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.18: 4 residues within 4Å: Chain G: I.374, F.375, N.376, R.480 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:K.95 NAG-NAG-BMA-MAN.29: 3 residues within 4Å: Chain L: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.25: 13 residues within 4Å: Chain L: V.224, S.225, E.227, P.228, L.277, N.278, G.393, I.450, R.451, G.452, S.457, S.458 Ligands: NAG-NAG.33 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.26: 5 residues within 4Å: Chain L: N.292, I.293, T.294, D.295 Chain M: Q.53 No protein-ligand interaction detected (PLIP)

3 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.34: 14 residues within 4Å: Chain B: A.1, V.2, F.11, L.26, T.27, A.30, V.72, I.92 Chain K: L.76, R.77, Q.80, L.81, I.84, E.143 8 PLIP interactions: 3 interactions with chain K, 5 interactions with chain B Hydrophobic interactions: K:R.77, K:L.81, B:A.1, B:V.2, B:F.11, B:F.11, B:V.72 Hydrogen bonds: K:E.143 LMT.39: 11 residues within 4Å: Chain B: L.76, R.77, Q.80, E.143 Chain H: F.11, S.23, L.26, T.27, A.30, Y.75, I.92 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain H Hydrophobic interactions: B:Q.80, H:F.11, H:Y.75 Hydrogen bonds: H:S.23 LMT.52: 6 residues within 4Å: Chain H: L.76, R.77, Q.80, L.81 Chain K: L.26, A.30 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:L.81

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

NAG.35: 4 residues within 4Å: Chain B: N.100, S.102, W.103, H.130 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.105 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.109, E.110, D.113, N.114 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.126, Y.127 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: G.16, S.17 Chain C: N.93 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: N.354, W.409, T.412, R.413, Y.417 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.370 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: E.365, N.410, N.411 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: N.93 Chain H: A.15, G.16, S.17 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: N.354, W.409, R.413 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.370 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain G: T.372, N.410 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain H: N.100, S.102, W.103 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain H: N.105 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain H: N.109, E.110, D.113, N.114 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain H: N.126, Y.127 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain K: N.100, S.102, W.103, H.130 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain K: N.105 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain K: N.109, E.110, D.113, N.114 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain K: N.126, Y.127 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain K: G.16, S.17 Chain L: G.92, N.93 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain L: N.354, W.409, R.413 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain L: N.370 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain L: T.372, N.410, N.411 Ligand excluded by 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

17b Fab light chain: AFJ
Envelope glycoprotein gp41: BHK
Envelope glycoprotein gp160: CGL
T-cell surface glycoprotein CD4: DMO
17b Fab heavy chain: EIN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

F
I

J
O

B
B

H
E

K
K

C
A

G
D

L
J

D
C

M
M

O
F

E
H

I
G

N
N

17b Fab light chain

Envelope glycoprotein gp41

Envelope glycoprotein gp160

T-cell surface glycoprotein CD4

17b Fab heavy chain

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