Research workbench
Crystal structure of a creatinine amidohydrolase (NPUN_F1913) from nostoc punctiforme pcc 73102 at 2.00 a resolution
Analyse Crystal structure of a creatinine amidohydrolase (NPUN_F1913) from nostoc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NO4
- Type
- protein
- Length
- 770 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creatinine amidohydrolase
- UniProt
- B2J3U5
- Ligands
- UNL, NI, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Creatinine amidohydrolase | protein | 264 | 55% helix, 11% strand | B2J3U5 |
| B | Creatinine amidohydrolase | protein | 256 | 54% helix, 11% strand | B2J3U5 |
| C | Creatinine amidohydrolase | protein | 250 | 56% helix, 12% strand | B2J3U5 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.83 | 0.91 | 55 | EDO |
| 2 | 984 | 0.75 | 0.78 | 92 | UNL, EDO, NI |
| 3 | 54 | 0.73 | 0.99 | 16 | empty |
| 4 | 88 | 0.69 | 0.93 | 22 | EDO |
| 5 | 209 | 0.53 | 0.78 | 30 | UNL |
Interfaces
3 interfaces between chains.
- A–B · 2462 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1294 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 156 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3NO4 · Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC… · 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 B2J3U5
- Elsewhere: RCSB PDB 3NO4 · PDBe 3NO4 · UniProt B2J3U5
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