MolNFT v1 · #185858 · protein

Structure of human C3B in complex with the ewe nanobody

7QIV · Complement C3 beta chain: “Structure of human C3B in complex with the ewe nanobody”. X-ray diffraction, 1 ligand (NAG), 16 pockets (best druggability 0.79). MolNFT v1 #185858 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7QIV
Type: protein
Length: 1,665 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C3 beta chain; Complement C3B alpha' chain; Nanobody ewe
UniProt: P01024
Ligands: NAG
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C3 beta chain	protein	638	7% helix, 50% strand	P01024
B	Complement C3B alpha' chain	protein	903	24% helix, 32% strand	P01024
C	Nanobody ewe	protein	124	7% helix, 48% strand	—

Ligands and binding sites

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

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

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1165	0.79	0.80	90	empty
2	58	0.72	0.98	22	empty
3	428	0.72	0.82	44	empty
4	138	0.64	0.87	25	empty
5	544	0.64	0.76	41	empty

Interfaces

2 interfaces between chains.

A–B · 5575 Å² buried · 77 hydrogen bonds · protein-protein
B–C · 706 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7QIV · Structure of human C3b in complex with the EWE nanobody · 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 0.97

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 7QIV · PDBe 7QIV · UniProt P01024

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