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W154F mutant creatininase

Analyse W154F mutant creatininase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3A6G
Type: protein
Length: 1,535 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 0.84

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F	Creatinine amidohydrolase (EC 3.5.2.10)	protein	257	48% helix, 12% strand	P83772
B	Creatinine amidohydrolase (EC 3.5.2.10)	protein	253	48% helix, 12% strand	P83772
C	Creatinine amidohydrolase (EC 3.5.2.10)	protein	254	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

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	1024	0.84	0.85	105	MN
2	1033	0.82	0.83	87	empty
3	1082	0.79	0.81	86	MN
4	1105	0.79	0.80	110	MN
5	59	0.74	0.99	14	empty

Interfaces

12 interfaces between chains.

A–F · 2036 Å² buried · 47 hydrogen bonds · protein-protein
D–E · 2000 Å² buried · 46 hydrogen bonds · protein-protein
B–C · 1985 Å² buried · 48 hydrogen bonds · protein-protein
E–F · 1475 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1459 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

3A6G · W154F 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 3A6G · PDBe 3A6G · UniProt P83772

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