MolNFT v1 · #115004 · protein

PROTEIN C

5C6P: “PROTEIN C”. X-ray diffraction, 1 ligand (4YH), 10 pockets (best druggability 0.83). MolNFT v1 #115004 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C6P
Type: protein
Length: 550 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein C; Protein D
UniProt: Q5F9J8, M1E1G6
Ligands: 4YH
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein C	protein	459	40% helix, 0% strand	Q5F9J8
B	Protein D	protein	91	0% helix, 22% strand	M1E1G6

Ligands and binding sites

4YH · (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl) pentanenitrile · ligand · chains A

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.83	0.83	76	empty
2	224	0.75	0.90	31	empty
3	219	0.65	0.83	34	empty
4	74	0.63	0.91	22	empty
5	121	0.50	0.80	30	empty

Interfaces

1 interface between chains.

A–B · 491 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5C6P · protein C · the same entry in another collection · chain A 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 Q5F9J8
Every structure of UniProt M1E1G6
Elsewhere: RCSB PDB 5C6P · PDBe 5C6P · UniProt Q5F9J8 · UniProt M1E1G6

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