Research workbench

Creatininase mn

Analyse Creatininase mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1J2T
Type: protein
Length: 1,542 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Creatinine amidohydrolase
EC: 3.5.2.10
UniProt: P83772
Ligands: ZN, MN, SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Creatinine amidohydrolase (EC 3.5.2.10)	protein	257	48% helix, 12% strand	P83772

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1160	0.82	0.83	102	MN
2	931	0.81	0.83	84	empty
3	1001	0.80	0.81	71	empty
4	1023	0.79	0.80	71	MN
5	58	0.74	0.99	14	empty

Interfaces

12 interfaces between chains.

B–C · 1989 Å² buried · 48 hydrogen bonds · protein-protein
A–F · 1971 Å² buried · 47 hydrogen bonds · protein-protein
D–E · 1946 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 1486 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 1483 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1J2T · Creatininase Mn · the same entry in another collection · chain F against F, TM-score 1.00
P83772 · AlphaFold monomer V2.0 prediction for creatinine amidohydrolase (P83772) · a predicted model of the same protein · chain E 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 P83772
Elsewhere: RCSB PDB 1J2T · PDBe 1J2T · UniProt P83772

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