MolNFT v1 · #103005 · protein

Crystal structure of the human C5AR antagonist C5A-A8

4P39 · Complement C5: “Crystal structure of the human C5AR antagonist C5A-A8”. X-ray diffraction, 5 pockets (best druggability 0.47). MolNFT v1 #103005 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P39
Type: protein
Length: 275 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C5
UniProt: P01031
Pockets: 5 · best druggability 0.47

Structure

x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Complement C5	protein	69	70% helix, 0% strand	P01031
C	Complement C5	protein	69	72% helix, 0% strand	P01031
D	Complement C5	protein	68	72% helix, 0% strand	P01031

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	168	0.47	0.76	27	empty
2	154	0.45	0.76	20	empty
3	151	0.44	0.75	23	empty
4	113	0.41	0.76	17	empty
5	105	0.38	0.75	15	empty

Interfaces

4 interfaces between chains.

A–B · 651 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 193 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 147 Å² buried · 1 hydrogen bond · protein-protein
C–D · 19 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4P39 · Crystal structure of the human C5aR antagonist C5a-A8 · 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 D against A, TM-score 0.73

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
Elsewhere: RCSB PDB 4P39 · PDBe 4P39 · UniProt P01031

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