SMTL ID : 7lok.1

Structure of CD4 mimetic M48U1 in complex with BG505 SOSIP.664 HIV-1 Env trimer and 17b Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-2-3-mer

Ligands

1 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: 15 residues within 4Å: Chain A: V.176, S.177, E.179, V.222, N.230, F.343, N.344, G.346, I.405, Q.406, G.407, R.410, C.411, V.412, S.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.410, A:E.179

1 x NAG- NAG- BMA- MAN- MAN: 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.2: 13 residues within 4Å: Chain C: S.177, F.178, E.179, P.180, N.230, N.344, C.345, G.346, I.405, R.410, C.411, S.413 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.410, C:R.410, C:G.346

1 x NAG- NAG- BMA- MAN: 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.3: 10 residues within 4Å: Chain L: V.176, S.177, F.178, N.230, N.344, C.345, G.346, R.410, V.412, S.413 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:F.178, L:V.176, L:G.346

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

NAG.4: 5 residues within 4Å: Chain A: N.230, P.259, V.412, S.413, N.414 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.412 Hydrogen bonds: A:N.414 NAG.5: 2 residues within 4Å: Chain C: E.55, N.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.56 NAG.6: 2 residues within 4Å: Chain C: N.202, T.204 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.204 NAG.7: 3 residues within 4Å: Chain C: H.297, N.299, S.379 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.297, C:N.299 NAG.8: 1 residues within 4Å: Chain C: N.306 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain C: N.230, P.259, S.413, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain C: N.263 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.263 NAG.11: 3 residues within 4Å: Chain L: N.263, V.300, S.301 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:N.263

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: ACL
Envelope Glycoprotein BG505 SOSIP.664 gp41: BDK
17b Fab Light Chain: EG
17b Fab Heavy Chain: FH
M48U1: IJM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

L
E

B
D

D
B

K
F

E
J

G
L

F
K

H
M

I
G

J
H

M
I

Envelope glycoprotein BG505 SOSIP.664 gp120

Envelope Glycoprotein BG505 SOSIP.664 gp41

17b Fab Light Chain

17b Fab Heavy Chain

M48U1

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