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Crystal structure of the mouse C5A anaphylatoxin

Analyse Crystal structure of the mouse C5A anaphylatoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P3A
Type: protein
Length: 276 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C5
UniProt: P06684
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C5	protein	70	67% helix, 0% strand	P06684
B	Complement C5	protein	69	67% helix, 0% strand	P06684
C	Complement C5	protein	68	71% helix, 0% strand	P06684
D	Complement C5	protein	69	67% helix, 0% strand	P06684

Ligands and binding sites

FMT · Formic acid · additive · 16 copies · chains A, B, C, D

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.81	0.98	22	FMT
2	120	0.80	0.98	22	FMT
3	105	0.36	0.73	18	empty

Interfaces

3 interfaces between chains.

C–D · 666 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 666 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 410 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4P3A · Crystal structure of the mouse C5a anaphylatoxin · the same entry in another collection · chain D against D, TM-score 1.00
P06684 · AlphaFold monomer V2.0 prediction for complement C5 (P06684) · a predicted model of the same protein · chain D against A, TM-score 0.86

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 P06684
Elsewhere: RCSB PDB 4P3A · PDBe 4P3A · UniProt P06684

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