MolNFT v1 · #188506 · protein

Human complement component C3B in complex with apl-1030

7TV9 · Complement C3 beta chain: “Human complement component C3B in complex with apl-1030”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.77). MolNFT v1 #188506 on GenesisL1: 3D structure, binding sites and…

PDB: 7TV9
Type: protein
Length: 1,601 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C3 beta chain; Complement C3B alpha' chain; Apl-1030 nanofitin
UniProt: P01024
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C3 beta chain	protein	636	6% helix, 46% strand	P01024
B	Complement C3B alpha' chain	protein	902	23% helix, 26% strand	P01024
C	Apl-1030 nanofitin	protein	63	27% helix, 40% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
BMA · beta-D-mannopyranose · sugar

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1198	0.77	0.79	85	empty
2	55	0.72	0.98	20	empty
3	459	0.72	0.82	45	empty
4	564	0.68	0.78	72	empty
5	198	0.57	0.80	29	empty

Interfaces

2 interfaces between chains.

A–B · 5060 Å² buried · 62 hydrogen bonds · protein-protein
A–C · 1194 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7TV9 · Human complement component C3B in complex with apl-1030 · 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 0.98

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 7TV9 · PDBe 7TV9 · UniProt P01024

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