MolNFT v1 · #146573 · protein
2.2 ångström resolution crystal structure of P-hydroxybenzoate hydroxylase from pseudomonas putida in complex with FAD.
6DLL: “2.2 ångström resolution crystal structure of P-hydroxybenzoate hydroxylase from pseudomonas putida in complex…”. X-ray diffraction, 2 ligands (FAD, CL), 19 pockets (best druggability 0.83). MolNFT v1 #146573 on GenesisL1: 3D…
- PDB
- 6DLL
- Type
- protein
- Length
- 1,589 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-hydroxybenzoate hydroxylase
- EC
- 1.14.13.2
- UniProt
- Q88H28
- Ligands
- FAD, CL
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | P-hydroxybenzoate hydroxylase (EC 1.14.13.2) | protein | 397 | 40% helix, 28% strand | Q88H28 |
| B | P-hydroxybenzoate hydroxylase (EC 1.14.13.2) | protein | 398 | 40% helix, 27% strand | Q88H28 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D
- FMT · Formic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.83 | 0.84 | 100 | FAD |
| 2 | 1184 | 0.83 | 0.84 | 113 | FAD |
| 3 | 626 | 0.79 | 0.85 | 64 | FAD |
| 4 | 629 | 0.79 | 0.84 | 62 | FAD |
| 5 | 298 | 0.74 | 0.87 | 37 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1325 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1307 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 484 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 483 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DLL · 2.2 Angstrom Resolution Crystal Structure of P-Hydroxybenzoate Hydroxylase from… · 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 Q88H28
- Elsewhere: RCSB PDB 6DLL · PDBe 6DLL · UniProt Q88H28
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