Research workbench
E122Q mutant creatininase complexed with creatine
Analyse E122Q mutant creatininase complexed with creatine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A6J
- Type
- protein
- Length
- 1,532 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
- CRN, ZN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Creatinine amidohydrolase (EC 3.5.2.10) | protein | 257 | 48% helix, 12% strand | P83772 |
| B | Creatinine amidohydrolase (EC 3.5.2.10) | protein | 254 | 48% helix, 12% strand | P83772 |
| C, F | Creatinine amidohydrolase (EC 3.5.2.10) | protein | 255 | 47% helix, 12% strand | P83772 |
| D | Creatinine amidohydrolase (EC 3.5.2.10) | protein | 256 | 46% helix, 12% strand | P83772 |
| E | Creatinine amidohydrolase (EC 3.5.2.10) | protein | 255 | 47% helix, 12% strand | P83772 |
Ligands and binding sites
- CRN · N-[(E)-amino(imino)methyl]-N-methylglycine · ligand · 5 copies · chains A, B, C, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 13 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.81 | 0.83 | 78 | empty |
| 2 | 998 | 0.78 | 0.79 | 61 | empty |
| 3 | 949 | 0.77 | 0.79 | 61 | empty |
| 4 | 936 | 0.77 | 0.79 | 63 | empty |
| 5 | 62 | 0.74 | 0.99 | 14 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1928 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 1917 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 1916 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1510 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1509 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
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 3A6J · PDBe 3A6J · UniProt P83772
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