MolNFT v1 · #104025 · protein

Moac in complex with cpmp crystallized in space group P212121

4PYD · Molybdenum cofactor biosynthesis protein moac: “Moac in complex with cpmp crystallized in space group P212121”. X-ray diffraction, 1 ligand (8CS), 14 pockets (best druggability 0.81). MolNFT v1 #104025 on GenesisL1: 3D structure…

PDB: 4PYD
Type: protein
Length: 841 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Molybdenum cofactor biosynthesis protein moac
UniProt: W0KCK5
Ligands: 8CS
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 33% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Molybdenum cofactor biosynthesis protein moac	protein	142	33% helix, 33% strand	W0KCK5
B	Molybdenum cofactor biosynthesis protein moac	protein	140	36% helix, 33% strand	W0KCK5
C	Molybdenum cofactor biosynthesis protein moac	protein	154	31% helix, 29% strand	W0KCK5
D	Molybdenum cofactor biosynthesis protein moac	protein	150	31% helix, 30% strand	W0KCK5
E	Molybdenum cofactor biosynthesis protein moac	protein	133	27% helix, 33% strand	W0KCK5
F	Molybdenum cofactor biosynthesis protein moac	protein	122	42% helix, 31% strand	W0KCK5

Ligands and binding sites

8CS · (2r,4ar,5ar,11ar,12as)-8-amino-2-hydroxy-4A,5A,9,11,11A,12A-hexahydro[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridine-10,12(4H,6H)-dione 2-oxide · ligand · 4 copies · chains A, B, C, E, D, F
EDO · 1,2-ethanediol · additive · 2 copies · chains C, E, B, F
GOL · Glycerol · additive · 2 copies · chains C, E, D, F
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B, D

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

Pockets

14 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	156	0.81	0.97	24	EDO
2	439	0.75	0.84	42	empty
3	61	0.72	0.97	19	empty
4	368	0.71	0.83	37	empty
5	149	0.60	0.84	25	8CS

Interfaces

15 interfaces between chains.

C–E · 2014 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1712 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 1696 Å² buried · 11 hydrogen bonds · protein-protein
B–E · 877 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 869 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4PYD · MoaC in complex with cPMP crystallized in space group P212121 · 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 W0KCK5
Elsewhere: RCSB PDB 4PYD · PDBe 4PYD · UniProt W0KCK5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.