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Human C3C in complex with the inhibitor compstatin

Analyse Human C3C in complex with the inhibitor compstatin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QKI
Type: protein
Length: 2,246 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C3; Compstatin
UniProt: P01024
Ligands: ACE, NAG, K, BR, NH2
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 7 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C3	protein	631	7% helix, 50% strand	P01024
B	Complement C3	protein	184	2% helix, 56% strand	P01024
C	Complement C3	protein	292	17% helix, 41% strand	P01024
D	Complement C3	protein	632	6% helix, 50% strand	P01024
E	Complement C3	protein	186	2% helix, 55% strand	P01024
F	Complement C3	protein	295	18% helix, 39% strand	P01024
G, H	Compstatin	protein	13	0% helix, 15% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, G, D, H
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D
K · Potassium ion · metal · 5 copies · chains A, C, D, F
BR · Bromide ion · ion · 32 copies · chains A, G, B, C, D, H, E, F
NH2 · Amino group · ion · 2 copies · chains G, H
GOL · Glycerol · additive · 18 copies · chains A, B, C, D, E, F, H

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	930	0.74	0.78	67	BR
2	828	0.73	0.78	84	BR
3	812	0.72	0.77	58	empty
4	426	0.72	0.82	47	empty
5	422	0.72	0.83	46	empty

Interfaces

12 interfaces between chains.

A–B · 3517 Å² buried · 63 hydrogen bonds · protein-protein
D–E · 3515 Å² buried · 60 hydrogen bonds · protein-protein
B–C · 1221 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1202 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 738 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

2QKI · Human C3c in complex with the inhibitor compstatin · the same entry in another collection · chain H against H, TM-score 1.00
P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P01024
Elsewhere: RCSB PDB 2QKI · PDBe 2QKI · UniProt P01024

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