MolNFT v1 · #127930 · protein

Complement factor D

5NB7: “Complement factor D”. X-ray diffraction, 1 ligand (8NQ), 1 pocket (best druggability 0.43). MolNFT v1 #127930 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NB7
Type: protein
Length: 230 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement factor D
EC: 3.4.21.46
UniProt: P00746
Ligands: 8NQ
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement factor D (EC 3.4.21.46)	protein	230	9% helix, 36% strand	P00746

Ligands and binding sites

8NQ · 1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl) carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]indazole-3-carboxamide · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.43	0.76	27	8NQ

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5NB7 · Complement factor D · the same entry in another collection · chain A against A, TM-score 1.00
P00746 · AlphaFold monomer V2.0 prediction for complement factor D (P00746) · 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 P00746
Elsewhere: RCSB PDB 5NB7 · PDBe 5NB7 · UniProt P00746

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