MolNFT v1 · #57399 · protein

W174F mutant creatininase, type II

3A6F · Creatinine amidohydrolase: “W174F mutant creatininase, type II”. X-ray diffraction, 2 ligands (MN, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #57399 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A6F
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: MN, ZN
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Creatinine amidohydrolase (EC 3.5.2.10)	protein	258	49% helix, 12% strand	P83772
B, C, D, E	Creatinine amidohydrolase (EC 3.5.2.10)	protein	257	49% helix, 12% strand	P83772
F	Creatinine amidohydrolase (EC 3.5.2.10)	protein	256	48% 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
CAC · Cacodylate ion · additive · 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1063	0.82	0.83	107	MN, CAC
2	999	0.82	0.83	84	empty
3	1018	0.80	0.81	76	MN, CAC
4	934	0.79	0.81	76	MN, CAC
5	58	0.74	0.99	16	empty

Interfaces

12 interfaces between chains.

A–F · 2041 Å² buried · 48 hydrogen bonds · protein-protein
D–E · 2012 Å² buried · 48 hydrogen bonds · protein-protein
B–C · 1994 Å² buried · 44 hydrogen bonds · protein-protein
C–D · 1461 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1453 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

3A6F · W174F mutant creatininase, Type II · 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 0.99

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 3A6F · PDBe 3A6F · UniProt P83772

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