MolNFT v1 · #61411 · protein
Crystal structure of putative oxygenase (YP_001051978.1) from shewanella baltica OS155 at 2.26 a resolution
3DKQ · Pkhd-type hydroxylase SBAL_3634: “Crystal structure of putative oxygenase (YP_001051978.1) from shewanella baltica OS155 at 2.26 a resolution”. X-ray diffraction, 1 ligand (NI), 10 pockets (best druggability 0.78). MolNFT v1 #61411…
- PDB
- 3DKQ
- Type
- protein
- Length
- 658 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pkhd-type hydroxylase SBAL_3634
- EC
- 1.14.11.-
- UniProt
- A3D8P6
- Ligands
- NI
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pkhd-type hydroxylase SBAL_3634 (EC 1.14.11.-) | protein | 230 | 32% helix, 36% strand | A3D8P6 |
| B | Pkhd-type hydroxylase SBAL_3634 (EC 1.14.11.-) | protein | 207 | 36% helix, 31% strand | A3D8P6 |
| C | Pkhd-type hydroxylase SBAL_3634 (EC 1.14.11.-) | protein | 221 | 33% helix, 36% strand | A3D8P6 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- IMD · Imidazole · additive · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.78 | 0.82 | 73 | GOL |
| 2 | 166 | 0.67 | 0.87 | 34 | NI, IMD |
| 3 | 118 | 0.66 | 0.89 | 19 | empty |
| 4 | 161 | 0.64 | 0.85 | 25 | NI, IMD |
| 5 | 101 | 0.57 | 0.85 | 25 | NI, IMD |
Interfaces
3 interfaces between chains.
- A–B · 866 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 387 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3DKQ · Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at… · the same entry in another collection · chain A against A, TM-score 1.00
- A3D8P6 · AlphaFold monomer V2.0 prediction for pkhd-type hydroxylase SBAL_3634 (A3D8P6) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 A3D8P6
- Elsewhere: RCSB PDB 3DKQ · PDBe 3DKQ · UniProt A3D8P6
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