MolNFT v1 · #119180 · protein

Crystal structure of human complement C3B in complex with daf (CCP2-4)

5FOA · Complement C3 beta chain: “Crystal structure of human complement C3B in complex with daf (CCP2-4)”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #119180 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5FOA
Type: protein
Length: 3,466 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C3 beta chain; Complement C3B alpha chain; Decay accelerating factor, CD55
UniProt: P01024, P08174
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Complement C3 beta chain	protein	642	6% helix, 51% strand	P01024
B, D	Complement C3B alpha chain	protein	902	24% helix, 31% strand	P01024
E, F	Decay accelerating factor, CD55	protein	189	2% helix, 39% strand	P08174

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	862	0.84	0.86	94	empty
2	1126	0.82	0.83	135	empty
3	1070	0.82	0.83	118	empty
4	626	0.78	0.84	82	empty
5	995	0.77	0.79	70	empty

Interfaces

12 interfaces between chains.

A–B · 5404 Å² buried · 69 hydrogen bonds · protein-protein
C–D · 5327 Å² buried · 67 hydrogen bonds · protein-protein
D–F · 1143 Å² buried · 16 hydrogen bonds · protein-protein
A–F · 691 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 644 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 29 disulfide (disulfide).

Compared structures

5FOA · Crystal Structure of Human Complement C3b in complex with DAF (CCP2-4) · the same entry in another collection · chain F against F, 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 0.99
P08174 · AlphaFold monomer V2.0 prediction for complement decay-accelerating factor (P08174) · a predicted model of the same protein · chain E against A, TM-score 0.96

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
Every structure of UniProt P08174
Elsewhere: RCSB PDB 5FOA · PDBe 5FOA · UniProt P01024 · UniProt P08174

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