MolNFT v1 · #151951 · protein

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

6I2X: “Structure of complement C5 in complex with small molecule inhibitor and cvf”. Electron crystallography, 2 ligands (H1H, MG), 20 pockets (best druggability 0.86). MolNFT v1 #151951 on GenesisL1: 3D structure, binding sites and…

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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