MolNFT v1 · #162904 · protein

Crystal structure of disulphide-linked human C3D dimer

6RMT · Complement C3: “Crystal structure of disulphide-linked human C3D dimer”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.51). MolNFT v1 #162904 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RMT
Type: protein
Length: 599 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C3
UniProt: P01024
Ligands: CL
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C3	protein	301	63% helix, 2% strand	P01024
B	Complement C3	protein	298	63% helix, 2% strand	P01024

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.51	0.78	39	CL
2	181	0.46	0.75	23	empty
3	73	0.43	0.80	15	empty
4	131	0.41	0.75	19	empty
5	63	0.30	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 382 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6RMT · Crystal structure of disulphide-linked human C3d dimer · the same entry in another collection · chain A against A, 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 0.90

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 6RMT · PDBe 6RMT · UniProt P01024

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