SMTL ID : 5thr.1

Cryo-EM structure of a BG505 Env-sCD4-17b-8ANC195 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 8.90 Å

Oligo State

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

Ligands

3 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.1: 17 residues within 4Å: Chain D: K.202, N.204, P.208, I.247 Chain T: N.28, T.29, G.31, I.52, R.54, W.55, S.57, I.69, S.70, A.71, V.72, D.73, T.75 3 PLIP interactions: 2 interactions with chain T, 1 interactions with chain D Hydrogen bonds: T:S.57, T:I.69, T:A.71 Hydrophobic interactions: D:P.208 NAG-NAG-BMA-MAN.4: 10 residues within 4Å: Chain E: K.202, N.204, P.208, I.247 Chain R: T.29, R.54, W.55, I.69, S.70, D.73 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain E Hydrogen bonds: R:I.69 Hydrophobic interactions: E:P.208 NAG-NAG-BMA-MAN.7: 10 residues within 4Å: Chain F: K.202, N.204, P.208, I.247 Chain P: T.29, R.54, W.55, S.70, V.72, D.73 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.208

6 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: 8 residues within 4Å: Chain D: E.245, N.246, N.249, K.252 Chain T: Q.1, Y.25, G.26, G.76 2 PLIP interactions: 2 interactions with chain T Hydrophobic interactions: T:Y.25 Hydrogen bonds: T:G.26 NAG-NAG-BMA-MAN-MAN.3: 2 residues within 4Å: Chain D: N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 11 residues within 4Å: Chain E: E.245, N.246, N.249, K.252 Chain R: Q.1, H.3, Y.25, G.26, N.28, G.76, P.79 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:Q.1, R:G.26 NAG-NAG-BMA-MAN-MAN.6: 2 residues within 4Å: Chain E: N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 11 residues within 4Å: Chain F: E.245, N.246, N.249, K.252 Chain P: Q.1, H.3, Y.25, G.26, N.28, G.76, P.79 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.26 NAG-NAG-BMA-MAN-MAN.9: 3 residues within 4Å: Chain F: S.333, N.355, S.357 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-11-16

Peptides

BG505 SOSIP gp41: ABC
BG505 SOSIP gp120: DEF
T-cell surface glycoprotein CD4: GHI
17b Fab VL domain: JKL
17b Fab VH domain: MNO
8ANC195 G52K5 VH domain: PRT
8ANC195 G52K5 VL domain: QSU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

R
R

T
T

Q
Q

S
S

U
U

BG505 SOSIP gp41

BG505 SOSIP gp120

T-cell surface glycoprotein CD4

17b Fab VL domain

17b Fab VH domain

8ANC195 G52K5 VH domain

8ANC195 G52K5 VL domain

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