SMTL ID : 5kel.1

EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 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: 2 residues within 4Å: Chain A: N.196, E.197 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain G: N.196, E.197 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain M: N.196, E.197 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: N.236 Chain F: G.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain G: N.236 Chain L: G.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 2 residues within 4Å: Chain M: N.236 Chain R: G.30 No protein-ligand interaction detected (PLIP)

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.3: 2 residues within 4Å: Chain A: N.225, I.228 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 2 residues within 4Å: Chain G: N.225, I.228 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 2 residues within 4Å: Chain M: N.225, I.228 No protein-ligand interaction detected (PLIP)

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.4: 9 residues within 4Å: Chain A: E.124 Chain B: A.6, Q.7, P.8, N.62, T.65 Chain C: N.56 Chain H: L.28, F.34 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Q.7 Hydrogen bonds: C:N.56 NAG-NAG-BMA-MAN-MAN.8: 9 residues within 4Å: Chain G: E.124 Chain H: A.6, Q.7, P.8, N.62, T.65 Chain I: N.56 Chain N: L.28, F.34 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:N.56 Hydrophobic interactions: H:Q.7 NAG-NAG-BMA-MAN-MAN.12: 9 residues within 4Å: Chain B: L.28, F.34 Chain M: E.124 Chain N: A.6, Q.7, P.8, N.62, T.65 Chain O: N.56 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:Q.7 Hydrogen bonds: O:N.56

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

NAG.13: 1 residues within 4Å: Chain A: N.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.206 NAG.14: 1 residues within 4Å: Chain G: N.206 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.206 NAG.15: 1 residues within 4Å: Chain M: N.206 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M: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: AGM
Ebola surface glycoprotein, GP2: BHN
c2G4 variable Fab domain heavy chain: CIO
c2G4 variable Fab domain light chain: DJP
c13C6 variable Fab domain heavy chain: EKQ
c13C6 variable Fab domain light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

M
F

B
B

H
G

N
I

C
H

I
P

O
Q

D
L

J
T

P
U

E
C

K
J

Q
M

F
D

L
N

R
O

Ebola surface glycoprotein, GP1

Ebola surface glycoprotein, GP2

c2G4 variable Fab domain heavy chain

c2G4 variable Fab domain light chain

c13C6 variable Fab domain heavy chain

c13C6 variable Fab domain light chain

Related Entries With Identical Sequence