SMTL ID : 6mu7.1

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-818251 in Complex with Human Antibodies 3H109L and 35O22 at 3.1 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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, C:H.96, B:D.111, B:S.113, B:H.33, B:D.111 Hydrophobic interactions: B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.21: 21 residues within 4Å: Chain E: L.9, G.16, S.17 Chain F: 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 G: H.96, N.97 Chain H: E.57, N.58 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:H.96, F:G.112, F:T.115, F:D.111, F:S.113, F:H.33, F:D.111 Hydrophobic interactions: F:T.115 NAG-NAG-BMA-MAN-MAN-MAN.41: 21 residues within 4Å: Chain I: L.9, G.16, S.17 Chain J: 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 K: H.96, N.97 Chain L: E.57, N.58 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain J Hydrogen bonds: K:H.96, J:G.112, J:T.115, J:D.111, J:S.113, J:H.33, J:D.111 Hydrophobic interactions: J: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: 4 residues within 4Å: Chain D: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 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.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain H: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 11 residues within 4Å: Chain H: 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.42: 4 residues within 4Å: Chain L: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 11 residues within 4Å: Chain L: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.47 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 5 residues within 4Å: Chain D: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain D: N.232, L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain H: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain H: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 6 residues within 4Å: Chain H: N.232, L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 5 residues within 4Å: Chain L: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 3 residues within 4Å: Chain L: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 6 residues within 4Å: Chain L: N.232, L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA.43 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.6: 5 residues within 4Å: Chain D: T.267, R.296, H.299, N.301, R.412 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.296, D:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26: 5 residues within 4Å: Chain H: T.267, R.296, H.299, N.301, R.412 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.296, H:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.46: 5 residues within 4Å: Chain L: T.267, R.296, H.299, N.301, R.412 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.296, L:R.296

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

NAG.8: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.9: 9 residues within 4Å: Chain A: R.106, E.110, N.114, M.115 Chain B: Q.1, Y.32, L.108, L.109 Chain C: P.59 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: 7 residues within 4Å: Chain D: N.103, N.106, D.110, D.111, R.113, G.114, K.117 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain D: R.162, N.167, T.168 Chain H: R.278 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain D: N.204, T.206, S.244, E.245, I.247, H.321 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: N.246, T.248, N.249 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain D: N.324 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain D: N.332, S.333, N.355, S.357 Ligands: NAG.19 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.18 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain E: N.100, S.102 Ligand excluded by PLIP NAG.29: 9 residues within 4Å: Chain E: R.106, E.110, N.114, M.115 Chain F: Q.1, Y.32, L.108, L.109 Chain G: P.59 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain F: N.69 Ligand excluded by PLIP NAG.32: 7 residues within 4Å: Chain H: N.103, N.106, D.110, D.111, R.113, G.114, K.117 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain H: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain H: R.162, N.167, T.168 Chain L: R.278 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain H: N.204, T.206, S.244, E.245, I.247, H.321 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain H: N.246, T.248, N.249 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain H: N.324 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain H: N.332, S.333, N.355, S.357 Ligands: NAG.39 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG.38 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain I: N.100, S.102 Ligand excluded by PLIP NAG.49: 9 residues within 4Å: Chain I: R.106, E.110, N.114, M.115 Chain J: Q.1, Y.32, L.108, L.109 Chain K: P.59 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain I: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain J: N.69 Ligand excluded by PLIP NAG.52: 7 residues within 4Å: Chain L: N.103, N.106, D.110, D.111, R.113, G.114, K.117 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain L: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain D: R.278 Chain L: R.162, N.167, T.168 Ligand excluded by PLIP NAG.55: 6 residues within 4Å: Chain L: N.204, T.206, S.244, E.245, I.247, H.321 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain L: N.246, T.248, N.249 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain L: N.324 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain L: N.332, S.333, N.355, S.357 Ligands: NAG.59 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain L: N.355, S.357 Ligands: NAG.58 Ligand excluded by PLIP

3 x JYY: 4-{3-[{4-[(R)-cyano(phenyl)methyl]piperidin-1-yl}(oxo)acetyl]-4-methoxy-1H-pyrrolo[2,3-c]pyridin-7-yl}-N-(2-hydroxyethyl)-1,3-thiazole-2-carboxamide(Non-covalent)

JYY.20: 21 residues within 4Å: Chain D: I.79, W.82, D.83, L.86, K.87, T.172, V.225, E.339, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, R.397, 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:E.339, D:F.351, D:F.351, D:I.392, D:M.394, D:W.395 Hydrogen bonds: D:D.83, D:D.83, D:D.83, D:W.395, D:Q.400 JYY.40: 21 residues within 4Å: Chain H: I.79, W.82, D.83, L.86, K.87, T.172, V.225, E.339, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, R.397, Q.400, A.401, M.402, M.443 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:W.82, H:W.82, H:V.225, H:E.339, H:F.351, H:F.351, H:I.392, H:M.394, H:W.395 Hydrogen bonds: H:D.83, H:D.83, H:D.83, H:W.395, H:Q.400 JYY.60: 21 residues within 4Å: Chain L: I.79, W.82, D.83, L.86, K.87, T.172, V.225, E.339, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, R.397, Q.400, A.401, M.402, M.443 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:W.82, L:W.82, L:V.225, L:E.339, L:F.351, L:F.351, L:I.392, L:M.394, L:W.395 Hydrogen bonds: L:D.83, L:D.83, L:D.83, L:W.395, L:Q.400

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: AEI
35O22 scFv heavy chain portion: BFJ
35O22 scFv light chain portion: CGK
Envelope glycoprotein gp160: DHL
3H109L Fab heavy chain: MOQ
3H109L Fab light chain: NPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E
B

I
B

B
D

F
D

J
D

C
E

G
E

K
E

D
G

H
G

L
G

M
H

O
H

Q
H

N
L

P
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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