Research workbench
Creatininase-product complex
Analyse Creatininase-product complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V7Z
- 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
- Q52548
- Ligands
- CRN, MN, ZN, SO4
- Pockets
- 20 · best druggability 0.85
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 | Q52548 |
Ligands and binding sites
- CRN · N-[(E)-amino(imino)methyl]-N-methylglycine · ligand · 6 copies · chains A, B, C, D, E, F
- 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
- SO4 · Sulfate ion · ion · 18 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.85 | 0.86 | 114 | empty |
| 2 | 1075 | 0.81 | 0.82 | 88 | empty |
| 3 | 845 | 0.80 | 0.83 | 81 | empty |
| 4 | 1051 | 0.77 | 0.79 | 66 | empty |
| 5 | 56 | 0.73 | 0.99 | 14 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1947 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1945 Ų buried · 46 hydrogen bonds · protein-protein
- A–F · 1933 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1499 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1480 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 1V7Z · creatininase-product complex · the same entry in another collection · chain A 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 Q52548
- Elsewhere: RCSB PDB 1V7Z · PDBe 1V7Z · UniProt Q52548
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.