SMTL ID : 6mu6.1

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-814508 in Complex with Human Antibodies 3H109L and 35O22 at 3.2 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN.1: 21 residues within 4Å: Chain A: L.9, G.16, S.17 Chain B: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain C: H.96, N.97 Chain D: E.57, N.58 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.112, B:T.115, B:T.115, C:H.96, B:D.111, B:S.113, B:H.33, B:T.115 Hydrophobic interactions: B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.20: 21 residues within 4Å: Chain G: L.9, G.16, S.17 Chain H: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain I: H.96, N.97 Chain J: E.57, N.58 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:G.112, H:T.115, H:T.115, I:H.96, H:D.111, H:S.113, H:H.33, H:T.115 Hydrophobic interactions: H:T.115 NAG-NAG-BMA-MAN-MAN-MAN.39: 21 residues within 4Å: Chain M: L.9, G.16, S.17 Chain N: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain O: H.96, N.97 Chain P: E.57, N.58 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain O Hydrogen bonds: N:G.112, N:T.115, N:T.115, O:H.96, N:D.111, N:S.113, N:H.33, N:T.115 Hydrophobic interactions: N:T.115

6 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: 5 residues within 4Å: Chain D: V.104, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 11 residues within 4Å: Chain D: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 5 residues within 4Å: Chain J: V.104, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 11 residues within 4Å: Chain J: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 5 residues within 4Å: Chain P: V.104, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 11 residues within 4Å: Chain P: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.46 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 3 residues within 4Å: Chain D: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain J: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain J: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain J: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain J: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain P: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 4 residues within 4Å: Chain P: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 3 residues within 4Å: Chain P: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 5 residues within 4Å: Chain P: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.42 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.7: 21 residues within 4Å: Chain D: T.267, R.296, H.299, N.301, R.412 Chain E: Q.100, G.101, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain F: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.296, E:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26: 21 residues within 4Å: Chain J: T.267, R.296, H.299, N.301, R.412 Chain K: Q.100, G.101, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain L: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:R.296, K:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.45: 21 residues within 4Å: Chain P: T.267, R.296, H.299, N.301, R.412 Chain Q: Q.100, G.101, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain R: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain Q Hydrogen bonds: P:R.296, Q:V.108

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

NAG.9: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain B: N.69 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain D: T.102, N.103, N.106, R.113, K.117 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain D: N.204, S.244, E.245, I.247 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain D: N.246, T.248, N.249 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain D: N.324 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain D: N.332, S.333, N.355, S.357 Ligands: NAG.18 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.17 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain H: N.69 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain J: T.102, N.103, N.106, R.113, K.117 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain J: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain J: N.204, S.244, E.245, I.247 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain J: N.246, T.248, N.249 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain J: N.324 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain J: N.332, S.333, N.355, S.357 Ligands: NAG.37 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG.36 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain M: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain N: N.69 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain P: T.102, N.103, N.106, R.113, K.117 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain P: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain P: N.204, S.244, E.245, I.247 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain P: N.246, T.248, N.249 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain P: N.324 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain P: N.332, S.333, N.355, S.357 Ligands: NAG.56 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain P: N.355, S.357 Ligands: NAG.55 Ligand excluded by PLIP

3 x JYV: (2R)-{1-[{7-[2-({[3-(dimethylamino)propyl](methyl)amino}methyl)-1,3-thiazol-4-yl]-4-methoxy-1H-pyrrolo[2,3-c]pyridin-3-yl}(oxo)acetyl]piperidin-4-yl}(phenyl)acetonitrile(Non-covalent)

JYV.19: 19 residues within 4Å: Chain D: I.79, W.82, D.83, L.86, T.172, V.225, E.339, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, A.401, M.402, M.443 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.82, D:W.82, D:V.225, D:V.225, D:E.339, D:F.351, D:F.351, D:I.392, D:W.395, D:W.395 Hydrogen bonds: D:W.395, D:Q.400, D:A.401 Salt bridges: D:D.83 JYV.38: 19 residues within 4Å: Chain J: I.79, W.82, D.83, L.86, T.172, V.225, E.339, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, A.401, M.402, M.443 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:W.82, J:W.82, J:V.225, J:V.225, J:E.339, J:F.351, J:F.351, J:I.392, J:W.395, J:W.395 Hydrogen bonds: J:W.395, J:Q.400, J:A.401 Salt bridges: J:D.83 JYV.57: 19 residues within 4Å: Chain P: I.79, W.82, D.83, L.86, T.172, V.225, E.339, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, A.401, M.402, M.443 14 PLIP interactions: 14 interactions with chain P Hydrophobic interactions: P:W.82, P:W.82, P:V.225, P:V.225, P:E.339, P:F.351, P:F.351, P:I.392, P:W.395, P:W.395 Hydrogen bonds: P:W.395, P:Q.400, P:A.401 Salt bridges: P:D.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lai, Y.T. et al., Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry. Nat Commun (2019)

Release Date

2019-01-16

Peptides

Envelope glycoprotein gp160: AGM
35O22 scFv heavy chain portion: BHN
35O22 scFv light chain portion: CIO
Envelope glycoprotein gp160: DJP
3H109L Fab heavy chain: EKQ
3H109L Fab light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
B

M
B

B
D

H
D

N
D

C
E

I
E

O
E

D
G

J
G

P
G

E
H

K
H

Q
H

F
L

L
L

R
L

Envelope glycoprotein gp160

35O22 scFv heavy chain portion

35O22 scFv light chain portion

Envelope glycoprotein gp160

3H109L Fab heavy chain

3H109L Fab light chain

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