9d8y.1 | SWISS-MODEL Template Library

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SMTL ID : 9d8y.1

Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.06 Å

Oligo State

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

Ligands

3 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.1:	7 residues within 4Å: Chain A: N.56 Chain D: G.16, T.18, A.21 Chain G: Y.102 Chain H: N.31, Y.50 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.21
NAG-NAG-BMA-MAN-MAN.2:	4 residues within 4Å: Chain B: N.56 Chain E: T.18 Chain I: Y.102 Chain J: Y.50 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Y.50, J:Y.50
NAG-NAG-BMA-MAN-MAN.3:	8 residues within 4Å: Chain C: E.55, N.56 Chain F: S.17, D.113 Chain K: Y.102 Chain L: Y.49, Y.50, T.53 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain L Hydrogen bonds: F:D.113 Hydrophobic interactions: L:T.53

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

NAG-NAG.4:

2 residues within 4Å:

Chain D: N.100, S.102

No protein-ligand interaction detected (PLIP)

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

NAG.5:	2 residues within 4Å: Chain E: N.100, S.102 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.100, E:S.102
NAG.6:	1 residues within 4Å: Chain F: N.100 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Thakur, B. et al., Cryo-EM structure of HIV-1 BG505 SOSIP.664 Env bound to 3-sCD4, 3-VRC34.01 Fab with one gp120 rotated. To Be Published

Release Date

2025-04-30

Peptides

Envelope glycoprotein gp160: ABC
Envelope glycoprotein gp160: DEF
VRC34.01 Fab Heavy Chain: GIK
VRC34.01 Fab Light Chain: HJL
T-cell surface glycoprotein CD4: MNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

I
I

K
K

H
H

J
J

L
L

M
M

N
N

O
O

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Envelope glycoprotein gp160

Envelope glycoprotein gp160

VRC34.01 Fab Heavy Chain

Toggle Identical (GIK)

VRC34.01 Fab Light Chain

Toggle Identical (HJL)

T-cell surface glycoprotein CD4

Toggle Identical (MO)

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