SMTL ID : 6u0l.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 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.355, S.357 Chain G: Y.110 Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.246, T.248 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.355, S.357 Chain H: Y.110 Ligands: NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP)

2 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.2: 15 residues within 4Å: Chain A: S.179, V.224, L.231, N.232, F.345, N.346, C.347, G.348, I.407, Q.408, G.409, V.410, C.413, V.414, S.415 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348, A:Q.408, A:V.410 NAG-NAG-BMA-MAN-MAN.7: 16 residues within 4Å: Chain C: V.178, P.182, K.222, V.224, L.231, N.232, F.345, N.346, C.347, G.348, I.407, Q.408, G.409, V.410, C.413, V.414 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.414 Hydrogen bonds: C:C.347, C:V.414, C:Q.408, C:G.409, C:V.410

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.5: 15 residues within 4Å: Chain B: S.179, L.231, N.232, F.345, C.347, G.348, I.407, Q.408, G.409, V.410, R.412, C.413, V.414, S.415 Ligands: NAG.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.414 Hydrogen bonds: B:R.412

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

NAG.8: 4 residues within 4Å: Chain A: N.332, T.341, S.357 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.232, P.261, V.414, N.416 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: K.304, N.308 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: E.57, N.58 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.204, T.206, E.245 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.308 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: T.267, H.299, N.301, T.383 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: N.332, T.341, S.357 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: P.261, N.416 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain C: Q.263, N.265, N.301, S.303, R.412, V.414 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain C: N.355, S.357, G.358 Chain K: Y.110 Ligands: NAG.26 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: E.57, N.58 Chain O: A.15 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.332, S.357 Ligands: NAG.24 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.361 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain M: N.126 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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