SMTL ID : 7lo6.1

Structure of CD4 mimetic BNM-III-170 in complex with BG505 SOSIP.664 HIV-1 Env trimer and 17b Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

7 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: 3 residues within 4Å: Chain A: N.353, S.355 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: N.202, S.242 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.244, T.246 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.353, S.355 Ligands: NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain E: N.244, I.245, T.246 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain E: N.306 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain E: N.353 Ligands: NAG.35 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: 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.2: 10 residues within 4Å: Chain A: E.179, K.220, N.230, F.343, C.345, G.346, I.405, Q.406, C.411, V.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.346

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.4: 14 residues within 4Å: Chain C: V.176, E.179, N.230, F.343, N.344, C.345, G.346, I.405, Q.406, G.407, V.408, R.410, C.411, V.412 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.412 Hydrogen bonds: C:G.346

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.7: 15 residues within 4Å: Chain E: V.176, S.177, F.178, E.179, V.222, N.230, N.344, G.346, I.405, Q.406, V.408, C.411, V.412, S.413 Ligands: NAG.37 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.412 Hydrogen bonds: E:V.412

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

NAG.11: 3 residues within 4Å: Chain A: N.202, T.204, H.319 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.244, T.246 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.263, R.410 Ligands: NAG.14 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: T.265, N.299, R.410 Ligands: NAG.13 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.306, W.362 Ligand excluded by PLIP NAG.16: 7 residues within 4Å: Chain A: N.330, S.331, S.332, G.333, T.339 Ligands: NAG-NAG.1, NAG-NAG.1 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.359, S.360, T.361 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: S.413, N.414 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: E.55, N.56 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.263, R.410 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: H.297, N.299, S.379, T.381 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.306 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.322 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: N.330, T.339 Ligands: NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.359, S.360, T.361 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.230, L.233, P.259, N.414 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: E.123, N.126 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: E.55, N.56 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: N.202, T.204, H.319 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.263, S.301, R.410 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: N.263, H.297, N.299, R.410 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.322 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain E: N.330, T.339, N.353 Ligands: NAG-NAG.10, NAG-NAG.10 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain E: N.359 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.7 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.107, E.110 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.126, Y.127 Ligand excluded by PLIP

3 x 5VG: ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide(Non-covalent)(Covalent)

5VG.19: 14 residues within 4Å: Chain A: S.224, T.225, N.251, S.342, F.343, N.344, N.391, M.392, W.393, R.395, I.396, G.397, G.438, G.439 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.393 Hydrogen bonds: A:N.391, A:R.395, A:G.397, A:G.439 Halogen bonds: A:S.342 5VG.28: 12 residues within 4Å: Chain C: V.223, S.224, F.343, N.344, F.349, N.391, M.392, W.393, R.395, I.396, G.397, G.439 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.393 Hydrogen bonds: C:N.391, C:R.395, C:G.397, C:G.439 5VG.38: 13 residues within 4Å: Chain E: T.225, E.337, V.338, S.342, F.343, F.349, N.391, M.392, W.393, R.395, I.396, G.397, G.439 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:V.338, E:W.393 Hydrogen bonds: E:N.391, E:M.392, E:R.395, E:G.397, E:G.439

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jette, C.A. et al., Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation. Nat Commun (2021)

Release Date

2021-04-14

Peptides

Envelope glycoprotein BG505 SOSIP.664 gp120: ACE
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41: BDF
17b Fab Light Chain: GIK
17b Fab Heavy Chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

I
I

K
K

H
H

J
J

L
L

Envelope glycoprotein BG505 SOSIP.664 gp120

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

17b Fab Light Chain

17b Fab Heavy Chain

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