SMTL ID : 5ken.1

EBOV GP in complex with variable Fab domains of IgGs c4G7 and c13C6

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-2-2-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: K.123, E.124, A.126 Chain B: P.7, N.61 Chain F: W.29, F.33 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.7 Hydrogen bonds: B:Q.6 NAG-NAG-BMA-MAN-MAN.3: 7 residues within 4Å: Chain E: K.123, E.124 Chain F: Q.6, P.7, N.61, T.64 Chain L: W.29 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Q.6 Hydrogen bonds: F:Q.6 NAG-NAG-BMA-MAN-MAN.4: 9 residues within 4Å: Chain B: W.29 Chain K: K.123, E.124, G.125, A.126 Chain L: Q.6, P.7, N.61, T.64 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:Q.6 Hydrogen bonds: L:Q.6

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

NAG-NAG.2: 2 residues within 4Å: Chain E: L.222, N.225 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain K: N.236 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain K: L.222, N.225 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain E: N.206 Chain J: D.58 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain K: E.197 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:E.197 NAG.9: 1 residues within 4Å: Chain K: N.206 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.206, K:N.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pallesen, J. et al., Structures of Ebola virus GP and sGP in complex with therapeutic antibodies. Nat Microbiol (2016)

Release Date

2016-09-07

Peptides

Ebola surface glycoprotein, GP1: AEK
Ebola surface glycoprotein, GP2: BFL
c4G7 variable Fab domain heavy chain: CGM
c4G7 variable Fab domain light chain: DHN
c13C6 variable Fab domain light chain: IO
c13C6 variable Fab domain heavy chain: JP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

K
K

B
B

F
F

L
M

C
C

G
G

M
N

D
D

H
H

N
O

I
I

O
P

J
J

P
Q

Ebola surface glycoprotein, GP1

Ebola surface glycoprotein, GP2

c4G7 variable Fab domain heavy chain

c4G7 variable Fab domain light chain

c13C6 variable Fab domain light chain

c13C6 variable Fab domain heavy chain

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