SMTL ID : 8de6.1

Oligomeric C9 in complex with aE11 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain C: G.521, T.523, A.534, C.535 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.521, C:C.535 NAG.5: 4 residues within 4Å: Chain F: G.521, T.523, A.534, C.535 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.521 NAG.9: 3 residues within 4Å: Chain G: G.521, T.523, A.534 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.521, G:G.521

6 x BMA: beta-D-mannopyranose(Post Translational Modification)

BMA.2: 3 residues within 4Å: Chain C: P.52, W.53, R.68 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.53, C:W.53 BMA.3: 5 residues within 4Å: Chain C: S.54, E.55, W.56, R.91 Chain D: S.75 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.54, C:E.55, C:W.56, C:R.91 BMA.6: 2 residues within 4Å: Chain F: W.53, R.68 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:W.53, F:R.68, F:R.68 BMA.7: 6 residues within 4Å: Chain A: D.73, G.74, S.75 Chain F: E.55, W.56, R.68 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:W.56, F:R.68, A:D.73, A:G.74 BMA.10: 3 residues within 4Å: Chain G: P.52, W.53, R.68 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:W.53, G:R.68 BMA.11: 4 residues within 4Å: Chain G: S.54, E.55, W.56, R.68 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:W.56, G:W.56, G:R.68

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain C: L.122, N.125, D.127, D.129, D.135, E.136 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.127, C:D.129, C:D.135, C:E.136 CA.8: 6 residues within 4Å: Chain F: L.122, N.125, D.127, D.129, D.135, E.136 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:L.122, F:D.127, F:D.129, F:D.135 CA.12: 6 residues within 4Å: Chain G: L.122, N.125, D.127, D.129, D.135, E.136 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.127, G:D.129, G:D.135, G:E.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bayly-Jones, C. et al., The neoepitope of the complement C5b-9 Membrane Attack Complex is formed by proximity of adjacent ancillary regions of C9. Commun Biol (2023)

Release Date

2023-01-25

Peptides

aE11 Fab VH: AD
aE11 Fab VL: BE
Complement component C9: CFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

D
B

B
F

E
I

C
A

F
C

G
G

aE11 Fab VH

aE11 Fab VL

Complement component C9