SMTL ID : 6mtj.1

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-378806 in Complex with Human Antibodies 3H109L and 35O22 at 2.9 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 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: 20 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, 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: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:H.96, B:G.112, B:T.115, B:D.111, B:S.113, B:H.33, B:S.52, B:S.52 NAG-NAG-BMA-MAN-MAN-MAN.21: 20 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, 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, I:H.96, H:D.111, H:S.113, H:H.33, H:S.52, H:S.52 NAG-NAG-BMA-MAN-MAN-MAN.41: 20 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, 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, O:H.96, N:D.111, N:S.113, N:H.33, N:S.52, N:S.52

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, T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 10 residues within 4Å: Chain D: E.181, L.231, N.232, N.346, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348 NAG-NAG-BMA.22: 5 residues within 4Å: Chain J: V.104, T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 10 residues within 4Å: Chain J: E.181, L.231, N.232, N.346, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.27 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.348 NAG-NAG-BMA.42: 5 residues within 4Å: Chain P: V.104, T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.43: 10 residues within 4Å: Chain P: E.181, L.231, N.232, N.346, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.47 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.348

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

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: 5 residues within 4Å: Chain D: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain J: Q.263, N.265, N.301, 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.44: 5 residues within 4Å: Chain P: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 3 residues within 4Å: Chain P: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 5 residues within 4Å: Chain P: N.232, L.235, P.261, 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: 19 residues within 4Å: Chain D: T.267, R.296, H.299, N.301 Chain E: Q.100, 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 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:V.108, D:R.296, D:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26: 19 residues within 4Å: Chain J: T.267, R.296, H.299, N.301 Chain K: Q.100, 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 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:V.108, J:R.296, J:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.46: 19 residues within 4Å: Chain P: T.267, R.296, H.299, N.301 Chain Q: Q.100, 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 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain Q Hydrogen bonds: P:R.296, P:R.296, Q:V.108

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: 10 residues within 4Å: Chain A: R.106, E.110, N.114, M.115, Q.119 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: 5 residues within 4Å: Chain D: N.103, D.110, D.111, R.113, 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 J: R.278 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain D: N.204, T.206, S.244, E.245, I.247 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: 6 residues within 4Å: Chain D: N.332, S.333, T.341, 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 G: N.100, S.102 Ligand excluded by PLIP NAG.29: 10 residues within 4Å: Chain G: R.106, E.110, N.114, M.115, Q.119 Chain H: Q.1, Y.32, L.108, L.109 Chain I: P.59 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain G: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain H: N.69 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain J: N.103, D.110, D.111, R.113, K.117 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain J: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain J: R.162, N.167, T.168 Chain P: R.278 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain J: N.204, T.206, S.244, E.245, I.247 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain J: N.246, T.248, N.249 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain J: N.324 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain J: N.332, S.333, T.341, N.355, S.357 Ligands: NAG.39 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG.38 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.49: 10 residues within 4Å: Chain M: R.106, E.110, N.114, M.115, Q.119 Chain N: Q.1, Y.32, L.108, L.109 Chain O: P.59 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain M: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain N: N.69 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain P: N.103, D.110, D.111, R.113, K.117 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain P: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain D: R.278 Chain P: R.162, N.167, T.168 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain P: N.204, T.206, S.244, E.245, I.247 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain P: N.246, T.248, N.249 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain P: N.324 Ligand excluded by PLIP NAG.58: 6 residues within 4Å: Chain P: N.332, S.333, T.341, N.355, S.357 Ligands: NAG.59 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain P: N.355, S.357 Ligands: NAG.58 Ligand excluded by PLIP

3 x 83G: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione(Non-covalent)

83G.20: 15 residues within 4Å: Chain D: I.79, W.82, D.83, L.86, V.225, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, M.402 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.82, D:W.82, D:V.225, D:F.351, D:F.351, D:I.392, D:M.402 Hydrogen bonds: D:W.395 83G.40: 15 residues within 4Å: Chain J: I.79, W.82, D.83, L.86, V.225, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, M.402 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:W.82, J:W.82, J:V.225, J:F.351, J:F.351, J:I.392, J:M.402 Hydrogen bonds: J:W.395 83G.60: 15 residues within 4Å: Chain P: I.79, W.82, D.83, L.86, V.225, S.344, F.345, F.351, Y.353, I.392, N.393, M.394, W.395, Q.400, M.402 8 PLIP interactions: 8 interactions with chain P Hydrophobic interactions: P:W.82, P:W.82, P:V.225, P:F.351, P:F.351, P:I.392, P:M.402 Hydrogen bonds: P:W.395

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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