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Structure of complement C5 in complex with SSL7

Analyse Structure of complement C5 in complex with SSL7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KLS
Type: protein
Length: 3,482 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C5; Exotoxin 1
UniProt: P01031, Q6GJP2
Ligands: NAG, CD
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C5	protein	1622	17% helix, 29% strand	P01031
X, Y	Exotoxin 1	protein	191	13% helix, 32% strand	Q6GJP2
B	Complement C5	protein	1478	17% helix, 30% strand	P01031

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
CD · Cadmium ion · metal · 9 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1019	0.85	0.86	90	empty
2	1187	0.83	0.84	122	CD
3	716	0.83	0.87	82	CD
4	1035	0.80	0.82	116	empty
5	558	0.80	0.86	84	empty

Interfaces

3 interfaces between chains.

A–B · 1389 Å² buried · 16 hydrogen bonds · protein-protein
B–Y · 1061 Å² buried · 17 hydrogen bonds · protein-protein
A–X · 1055 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 25 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3KLS · Structure of complement C5 in complex with SSL7 · the same entry in another collection · chain A against A, TM-score 1.00
P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01031
Every structure of UniProt Q6GJP2
Elsewhere: RCSB PDB 3KLS · PDBe 3KLS · UniProt P01031 · UniProt Q6GJP2

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