MolNFT v1 · #184215 · protein
Crystal structure of synechocystis sp PCC6803 guanidinium hydrolase
7OI1 · Probable agmatinase 2: “Crystal structure of synechocystis sp PCC6803 guanidinium hydrolase”. X-ray diffraction, 2 ligands (NI, CL), 11 pockets (best druggability 0.78). MolNFT v1 #184215 on GenesisL1: 3D structure, binding sites…
- PDB
- 7OI1
- Type
- protein
- Length
- 1,134 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable agmatinase 2
- EC
- 3.5.3.11
- UniProt
- P73270
- Ligands
- NI, CL
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Probable agmatinase 2 (EC 3.5.3.11) | protein | 378 | 42% helix, 16% strand | P73270 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- CAC · Cacodylate ion · additive · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.78 | 0.83 | 58 | EDO |
| 2 | 199 | 0.70 | 0.87 | 38 | empty |
| 3 | 374 | 0.64 | 0.79 | 31 | empty |
| 4 | 214 | 0.63 | 0.83 | 33 | empty |
| 5 | 265 | 0.58 | 0.78 | 27 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 2433 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1880 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 982 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7OI1 · Crystal structure of Synechocystis sp PCC6803 guanidinium hydrolase · the same entry in another collection · chain A against A, TM-score 1.00
- P73270 · AlphaFold monomer V2.0 prediction for probable agmatinase 2 (P73270) · a predicted model of the same protein · chain A 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 P73270
- Elsewhere: RCSB PDB 7OI1 · PDBe 7OI1 · UniProt P73270
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