SMTL ID : 8b0f.1

CryoEM structure of C5b8-CD59

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-mer

Ligands

2 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: 8 residues within 4Å: Chain A: S.860, A.861, V.862, N.909, I.910, N.911, I.922, V.924 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain C: F.329, A.359, L.360, K.361 Chain D: E.241, N.243, R.281 No protein-ligand interaction detected (PLIP)

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

NAG-BMA.2: 7 residues within 4Å: Chain B: G.240, E.242, Q.244, N.324, F.325, T.326, S.368 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.242, B:N.324

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 8 residues within 4Å: Chain D: L.138, L.139, C.140, N.141, D.143, D.145, D.151, E.152 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:L.138, D:D.143, D:D.145, D:D.151, D:E.152 CA.5: 9 residues within 4Å: Chain E: L.113, V.114, C.115, N.116, D.118, Q.119, D.120, D.126, E.127 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:L.113, E:D.118, E:D.120, E:D.126, E:E.127

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

NAG.6: 2 residues within 4Å: Chain E: Q.436, N.437 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Couves, E.C. et al., Structural basis for membrane attack complex inhibition by CD59. Nat Commun (2023)

Release Date

2023-02-22

Peptides

Complement C5: A
Complement component C6: B
Complement component C7: C
Complement component C8 beta chain: D
Complement component C8 alpha chain: E
Complement component C8 gamma chain: F
CD59 glycoprotein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Complement C5

Complement component C6

Complement component C7

Complement component C8 beta chain

Complement component C8 alpha chain

Complement component C8 gamma chain

CD59 glycoprotein

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