SMTL ID : 6opo.1

Symmetric 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

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: 6 residues within 4Å: Chain A: W.101, N.250, S.252, G.253, P.254, S.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.254 NAG-NAG.2: 4 residues within 4Å: Chain A: E.88, V.90, N.245, N.257 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.88, A:V.90 NAG-NAG.4: 3 residues within 4Å: Chain A: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: E.309, N.311, N.347, I.348, S.349, R.455 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.10 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: V.386, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: K.350, P.403, N.406, D.416, P.418, E.422, N.424 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.350 Hydrogen bonds: A:E.422 NAG-NAG.11: 6 residues within 4Å: Chain F: W.101, N.250, S.252, G.253, P.254, S.290 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.254 NAG-NAG.12: 4 residues within 4Å: Chain F: E.88, V.90, N.245, N.257 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:E.88, F:V.90 NAG-NAG.14: 3 residues within 4Å: Chain F: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 8 residues within 4Å: Chain F: E.309, N.311, N.347, I.348, S.349, R.455 Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain F: T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.20 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain F: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain F: V.386, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain F: K.350, P.403, N.406, D.416, P.418, E.422, N.424 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.350 Hydrogen bonds: F:E.422 NAG-NAG.21: 6 residues within 4Å: Chain K: W.101, N.250, S.252, G.253, P.254, S.290 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:P.254 NAG-NAG.22: 4 residues within 4Å: Chain K: E.88, V.90, N.245, N.257 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:E.88, K:V.90 NAG-NAG.24: 3 residues within 4Å: Chain K: N.292, T.294, D.295 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 8 residues within 4Å: Chain K: E.309, N.311, N.347, I.348, S.349, R.455 Ligands: NAG-NAG-BMA.30, NAG-NAG-BMA.30 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain K: T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG-BMA.30 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain K: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain K: V.386, N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 7 residues within 4Å: Chain K: K.350, P.403, N.406, D.416, P.418, E.422, N.424 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:K.350 Hydrogen bonds: K:E.422

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.3: 15 residues within 4Å: Chain A: V.224, S.225, E.227, P.228, V.270, L.277, N.278, G.393, I.450, G.452, Q.453, R.455, S.457, S.458 Ligands: NAG.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.452, A:Q.453 NAG-NAG-BMA-MAN-MAN.13: 15 residues within 4Å: Chain F: V.224, S.225, E.227, P.228, V.270, L.277, N.278, G.393, I.450, G.452, Q.453, R.455, S.457, S.458 Ligands: NAG.41 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.452, F:Q.453 NAG-NAG-BMA-MAN-MAN.23: 15 residues within 4Å: Chain K: V.224, S.225, E.227, P.228, V.270, L.277, N.278, G.393, I.450, G.452, Q.453, R.455, S.457, S.458 Ligands: NAG.48 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.452, K:Q.453

3 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.10: 6 residues within 4Å: Chain A: N.311, N.347, E.422, N.424 Ligands: NAG-NAG.5, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 6 residues within 4Å: Chain F: N.311, N.347, E.422, N.424 Ligands: NAG-NAG.15, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 6 residues within 4Å: Chain K: N.311, N.347, E.422, N.424 Ligands: NAG-NAG.25, NAG-NAG.26 No protein-ligand interaction detected (PLIP)

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

NAG.31: 5 residues within 4Å: Chain A: G.92, N.93 Chain C: A.15, G.16, S.17 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain A: N.354, W.409, R.413, T.414, D.415, Y.417 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain A: K.371, T.372, W.409, N.410, N.411 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.3 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.100, S.102 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.105 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain F: G.92, N.93 Chain H: A.15, G.16, S.17 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain F: N.354, W.409, R.413, T.414, D.415, Y.417 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain F: K.371, T.372, W.409, N.410, N.411 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain F: S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.13 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain H: N.105 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain K: G.92, N.93 Chain M: A.15, G.16, S.17 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain K: N.354, W.409, R.413, T.414, D.415, Y.417 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain K: K.371, T.372, W.409, N.410, N.411 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain K: S.457, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.23 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain M: N.105 Ligand excluded by PLIP

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

LMT.35: 14 residues within 4Å: Chain C: A.1, V.2, I.8, F.11, T.27, A.71, Y.75, K.90, I.92, C.93 Chain M: L.76, R.77, L.81, E.143 10 PLIP interactions: 3 interactions with chain M, 7 interactions with chain C Hydrophobic interactions: M:L.76, M:L.81, C:V.2, C:I.8, C:F.11, C:F.11, C:Y.75, C:Y.75 Hydrogen bonds: M:E.143, C:T.27 LMT.42: 14 residues within 4Å: Chain C: L.76, R.77, L.81, E.143 Chain H: A.1, V.2, I.8, F.11, T.27, A.71, Y.75, K.90, I.92, C.93 10 PLIP interactions: 7 interactions with chain H, 3 interactions with chain C Hydrophobic interactions: H:V.2, H:I.8, H:F.11, H:F.11, H:Y.75, H:Y.75, C:L.76, C:L.81 Hydrogen bonds: H:T.27, C:E.143 LMT.49: 14 residues within 4Å: Chain H: L.76, R.77, L.81, E.143 Chain M: A.1, V.2, I.8, F.11, T.27, A.71, Y.75, K.90, I.92, C.93 10 PLIP interactions: 7 interactions with chain M, 3 interactions with chain H Hydrophobic interactions: M:V.2, M:I.8, M:F.11, M:F.11, M:Y.75, M:Y.75, H:L.76, H:L.81 Hydrogen bonds: M:T.27, H:E.143

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
J

B
L

G
E

L
K

C
B

H
F

M
M

D
C

I
G

N
N

E
H

J
I

O
O

Envelope glycoprotein gp160

17b Fab light chain

Envelope glycoprotein gp41

T-cell surface glycoprotein CD4

17b Fab heavy chain

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