SMTL ID : 6mug.1

Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.8 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 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: 19 residues within 4Å: Chain A: L.9, 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: N.58 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.115, B:T.115, C:H.96, B:S.113, B:H.33, B:S.52, B:S.52, B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.20: 19 residues within 4Å: Chain G: L.9, 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: N.58 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:T.115, H:T.115, I:H.96, H:S.113, H:H.33, H:S.52, H:S.52, H:T.115 NAG-NAG-BMA-MAN-MAN-MAN.39: 19 residues within 4Å: Chain M: L.9, 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: N.58 5 PLIP interactions: 1 interactions with chain O, 4 interactions with chain N Hydrogen bonds: O:H.96, N:T.115, N:T.115, N:S.113, N:H.33, N:S.52, N:S.52, N:T.115

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

NAG-NAG.2: 4 residues within 4Å: Chain D: N.130, Y.147, D.301 Chain F: R.95 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 10 residues within 4Å: Chain D: E.192, P.193, L.242, N.243, F.355, N.356, G.358, C.421, S.422, S.423 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.358 NAG-NAG.21: 4 residues within 4Å: Chain J: N.130, Y.147, D.301 Chain L: R.95 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 10 residues within 4Å: Chain J: E.192, P.193, L.242, N.243, F.355, N.356, G.358, C.421, S.422, S.423 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.358 NAG-NAG.40: 4 residues within 4Å: Chain P: N.130, Y.147, D.301 Chain R: R.95 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 10 residues within 4Å: Chain P: E.192, P.193, L.242, N.243, F.355, N.356, G.358, C.421, S.422, S.423 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.358

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.4: 23 residues within 4Å: Chain D: T.278, R.307, H.310, N.312, N.389, R.420 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 Ligands: NAG.17 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:V.108, D:R.307, D:R.307 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.23: 23 residues within 4Å: Chain J: T.278, R.307, H.310, N.312, N.389, R.420 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 Ligands: NAG.36 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:R.307, J:R.307, K:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.42: 23 residues within 4Å: Chain P: T.278, R.307, H.310, N.312, N.389, R.420 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 Ligands: NAG.55 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain P Hydrogen bonds: Q:V.108, P:R.307, P:R.307

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

NAG.5: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain D: N.100, S.132, F.133, N.134, K.145 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain D: V.156, R.173, N.178 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain D: N.215, S.217, S.255, Q.332 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain D: N.210, K.212, N.222, E.248 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain D: N.257, T.259, D.260 Ligand excluded by PLIP NAG.12: 6 residues within 4Å: Chain D: E.274, N.276, N.312, I.313, S.314 Ligands: NAG.17 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain D: N.282, I.303, Q.418 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain D: I.339, N.341, H.342, R.445 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain D: N.365, T.367 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: P.368, N.371 Ligand excluded by PLIP NAG.17: 7 residues within 4Å: Chain D: N.312, E.387, Q.388, N.389, R.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG.12 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain D: R.233, N.243, N.424 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain G: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain J: N.100, S.132, F.133, N.134, K.145 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain J: V.156, R.173, N.178 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain J: N.215, S.217, S.255, Q.332 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain J: N.210, K.212, N.222, E.248 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain J: N.257, T.259, D.260 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain J: E.274, N.276, N.312, I.313, S.314 Ligands: NAG.36 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain J: N.282, I.303, Q.418 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain J: I.339, N.341, H.342, R.445 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain J: N.365, T.367 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain J: P.368, N.371 Ligand excluded by PLIP NAG.36: 7 residues within 4Å: Chain J: N.312, E.387, Q.388, N.389, R.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.23, NAG.31 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain J: R.233, N.243, N.424 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain M: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain P: N.100, S.132, F.133, N.134, K.145 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain P: V.156, R.173, N.178 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain P: N.215, S.217, S.255, Q.332 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain P: N.210, K.212, N.222, E.248 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain P: N.257, T.259, D.260 Ligand excluded by PLIP NAG.50: 6 residues within 4Å: Chain P: E.274, N.276, N.312, I.313, S.314 Ligands: NAG.55 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain P: N.282, I.303, Q.418 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain P: I.339, N.341, H.342, R.445 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain P: N.365, T.367 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain P: P.368, N.371 Ligand excluded by PLIP NAG.55: 7 residues within 4Å: Chain P: N.312, E.387, Q.388, N.389, R.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.42, NAG.50 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain P: R.233, N.243, N.424 Ligand excluded by PLIP

3 x JYS: 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione(Non-covalent)

JYS.19: 15 residues within 4Å: Chain D: I.78, I.79, W.82, D.83, V.236, S.354, F.361, Y.363, I.400, N.401, M.402, W.403, K.408, A.409, M.410 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.82, D:V.236, D:F.361, D:Y.363, D:I.400, D:M.402 Hydrogen bonds: D:D.83 JYS.38: 15 residues within 4Å: Chain J: I.78, I.79, W.82, D.83, V.236, S.354, F.361, Y.363, I.400, N.401, M.402, W.403, K.408, A.409, M.410 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:W.82, J:V.236, J:F.361, J:Y.363, J:I.400, J:M.402 Hydrogen bonds: J:D.83 JYS.57: 15 residues within 4Å: Chain P: I.78, I.79, W.82, D.83, V.236, S.354, F.361, Y.363, I.400, N.401, M.402, W.403, K.408, A.409, M.410 7 PLIP interactions: 7 interactions with chain P Hydrophobic interactions: P:W.82, P:V.236, P:F.361, P:Y.363, P:I.400, P:M.402 Hydrogen bonds: 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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