MolNFT v1 · #57401 · protein

W154A mutant creatininase

3A6H · Creatinine amidohydrolase: “W154A mutant creatininase”. X-ray diffraction, 3 ligands (MN, ZN, CL), 20 pockets (best druggability 0.83). MolNFT v1 #57401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A6H
Type: protein
Length: 1,539 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: MN, ZN, CL
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F	Creatinine amidohydrolase (EC 3.5.2.10)	protein	257	49% helix, 12% strand	P83772
B, C, E	Creatinine amidohydrolase (EC 3.5.2.10)	protein	256	49% helix, 12% strand	P83772

Ligands and binding sites

MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 6 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.83	0.84	79	MN, ZN, CL
2	998	0.82	0.83	86	empty
3	1143	0.82	0.83	80	MN, CL, ZN
4	1095	0.81	0.83	80	MN, ZN, CL
5	55	0.73	0.99	14	empty

Interfaces

12 interfaces between chains.

A–F · 1997 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 1985 Å² buried · 42 hydrogen bonds · protein-protein
D–E · 1942 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 1494 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 1482 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

3A6H · W154A mutant creatininase · 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 D 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 3A6H · PDBe 3A6H · UniProt P83772

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