MolNFT v1 · #53036 · protein

C3 convertase (C3BBB) stabilized by scin

2WIN · Complement C3 beta chain: “C3 convertase (C3BBB) stabilized by scin”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.81). MolNFT v1 #53036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2WIN
Type: protein
Length: 8,518 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C3 beta chain; Complement C3B alpha' chain; Complement factor B…
EC: 3.4.21.47
UniProt: P01024, P00751, Q6GFB4
Ligands: NAG, BMA, MAN, MG
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 22% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Complement C3 beta chain	protein	638	7% helix, 49% strand	P01024
B	Complement C3B alpha' chain	protein	901	24% helix, 29% strand	P01024
D	Complement C3B alpha' chain	protein	901	24% helix, 29% strand	P01024
F, H	Complement C3B alpha' chain	protein	900	24% helix, 28% strand	P01024
I, J, K, L	Complement factor B (EC 3.4.21.47)	protein	507	22% helix, 23% strand	P00751
M, N, P, Q	Staphylococcal complement inhibitor	protein	84	83% helix, 0% strand	Q6GFB4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
BMA · beta-D-mannopyranose · sugar · 21 copies · chains E
MAN · alpha-D-mannopyranose · sugar · 8 copies · chains G, A
MG · Magnesium ion · metal · 4 copies · chains D, I, H, J, F, K, B, L

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

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	901	0.81	0.83	65	empty
2	816	0.81	0.84	70	empty
3	789	0.81	0.84	72	empty
4	986	0.81	0.82	79	empty
5	1037	0.80	0.81	86	empty

Interfaces

38 interfaces between chains.

C–D · 5288 Å² buried · 64 hydrogen bonds · protein-protein
A–B · 5282 Å² buried · 66 hydrogen bonds · protein-protein
E–F · 5262 Å² buried · 64 hydrogen bonds · protein-protein
G–H · 5018 Å² buried · 57 hydrogen bonds · protein-protein
C–E · 1488 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 60 disulfide, 15 glycan (disulfide, N-glycosylation).

Compared structures

2WIN · C3 convertase (C3bBb) stabilized by SCIN · the same entry in another collection · chain K against K, TM-score 1.00

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 P00751
Every structure of UniProt Q6GFB4
Elsewhere: RCSB PDB 2WIN · PDBe 2WIN · UniProt P01024 · UniProt P00751 · UniProt Q6GFB4

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