SMTL ID : 6u0n.1

Asymmetrically open conformational state (Class II) of HIV-1 Env trimer BG505 SOSIP.664 in complex with sCD4 and E51 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 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: 4 residues within 4Å: Chain A: N.244, T.246, N.247 Chain D: K.90 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.353, S.355 Chain G: Y.110 Ligands: NAG.8 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.3: 17 residues within 4Å: Chain A: S.177, P.180, V.222, L.229, N.230, F.343, N.344, C.345, G.346, I.405, Q.406, V.408, R.410, C.411, V.412, S.413 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.408 NAG-NAG-BMA-MAN-MAN.4: 18 residues within 4Å: Chain B: V.176, S.177, P.180, V.222, L.229, N.230, F.343, N.344, C.345, G.346, I.405, Q.406, G.407, V.408, R.410, C.411, V.412 Ligands: NAG.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.406, B:G.407, B:V.408 NAG-NAG-BMA-MAN-MAN.5: 17 residues within 4Å: Chain C: S.177, P.180, L.229, N.230, N.344, C.345, G.346, I.405, Q.406, G.407, V.408, I.409, R.410, C.411, V.412, S.413 Ligands: NAG.26 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.346, C:Q.406, C:G.407, C:V.408

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

NAG.6: 2 residues within 4Å: Chain A: G.321, N.322 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.306 Ligand excluded by PLIP NAG.8: 6 residues within 4Å: Chain A: N.330, T.339, N.353, S.355 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.230, P.259, V.412, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.3 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: E.55, N.56 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.202, T.204, S.242, E.243 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain B: N.353, S.355, G.356, P.383 Chain H: Y.110 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: E.55, N.56 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.359 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.244, T.246, N.247 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: Q.261, N.263, S.301, R.410 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: T.265, H.297, N.299 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.330, S.332, S.355, N.359 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.306 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.244, T.246, N.247 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: Q.261, N.263, N.299, S.301 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: T.265, H.297, N.299, R.410 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.330, S.331, T.339, S.355 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.306 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain C: N.230, L.233, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain C: N.353, S.355, G.356, P.383 Chain K: Y.110 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.56 Chain O: G.16, S.17 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.359 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-12-11

Peptides

Envelope glycoprotein gp120: ABC
T-cell surface glycoprotein CD4: DEF
E51 Fab heavy chain: GHK
E51 Fab light chain: IJL
Envelope glycoprotein gp41: MNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

K
P

I
J

J
L

L
Q

M
X

N
Y

O
Z

Envelope glycoprotein gp120

T-cell surface glycoprotein CD4

E51 Fab heavy chain

E51 Fab light chain

Envelope glycoprotein gp41

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