Research workbench

Structure of complement C5 in complex with small molecule inhibitor and cvf

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

PDB: 6I2X
Type: protein
Length: 2,414 residues
Chains: 3
Method: electron crystallography
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C5; Cobra venom factor
UniProt: P01031, Q91132
Ligands: H1H, MG
Pockets: 20 · best druggability 0.86

Structure

electron crystallography · 3 distinct chains · 11% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Complement C5	protein	648	4% helix, 47% strand	P01031
A	Complement C5	protein	815	26% helix, 25% strand	P01031
B	Cobra venom factor	protein	951	4% helix, 44% strand	Q91132

Ligands and binding sites

H1H · 5-methoxy-2-[[(1~{S})-1-(2-methoxyphenyl) ethyl]carbamoylamino]-4-(4-methylpentoxy)benzoic acid · ligand · chains A
MG · Magnesium ion · metal · chains 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	1060	0.86	0.87	119	empty
2	976	0.82	0.83	89	H1H
3	748	0.76	0.81	74	empty
4	479	0.73	0.82	48	empty
5	629	0.72	0.79	53	empty

Interfaces

3 interfaces between chains.

C–A · 4945 Å² buried · 56 hydrogen bonds · protein-protein
C–B · 1486 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 736 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q91132 · AlphaFold monomer V2.0 prediction for cobra venom factor (Q91132) · a predicted model of the same protein · chain B against A, TM-score 0.83

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 Q91132
Elsewhere: RCSB PDB 6I2X · PDBe 6I2X · UniProt P01031 · UniProt Q91132

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