MolNFT v1 · #118793 · protein

Mouse complement factor D

5FCR: “Mouse complement factor D”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.76). MolNFT v1 #118793 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FCR
Type: protein
Length: 919 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement factor D
EC: 3.4.21.46
UniProt: P03953
Ligands: SO4
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Complement factor D (EC 3.4.21.46)	protein	230	8% helix, 35% strand	P03953
C	Complement factor D (EC 3.4.21.46)	protein	229	8% helix, 35% strand	P03953

Ligands and binding sites

SO4 · Sulfate ion · ion · chains C
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, C
DMS · Dimethyl sulfoxide · additive · 2 copies · chains D
GOL · Glycerol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	983	0.76	0.79	121	EPE
2	481	0.62	0.75	42	empty
3	60	0.28	0.74	15	empty

Interfaces

4 interfaces between chains.

A–C · 464 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 332 Å² buried · 1 hydrogen bond · protein-protein
B–D · 320 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 95 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5FCR · Mouse complement factor D · the same entry in another collection · chain D against D, TM-score 1.00
P03953 · AlphaFold monomer V2.0 prediction for complement factor D (P03953) · a predicted model of the same protein · chain C against A, 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 P03953
Elsewhere: RCSB PDB 5FCR · PDBe 5FCR · UniProt P03953

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