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Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase from burkholderia thailandensis
Analyse Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PNH
- Type
- protein
- Length
- 1,860 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D,D-heptose 1,7-bisphosphate phosphatase
- EC
- 3.1.3.-
- UniProt
- Q2T109
- Pockets
- 15 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | D,D-heptose 1,7-bisphosphate phosphatase (EC 3.1.3.-) | protein | 155 | 41% helix, 23% strand | Q2T109 |
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.59 | 0.88 | 16 | empty |
| 2 | 61 | 0.53 | 0.87 | 17 | empty |
| 3 | 109 | 0.52 | 0.82 | 25 | empty |
| 4 | 81 | 0.51 | 0.84 | 18 | empty |
| 5 | 56 | 0.49 | 0.86 | 16 | empty |
Interfaces
12 interfaces between chains.
- H–K · 965 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 880 Ų buried · 12 hydrogen bonds · protein-protein
- A–J · 811 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 805 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 568 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4PNH · Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase from Burkholderia… · 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 Q2T109
- Elsewhere: RCSB PDB 4PNH · PDBe 4PNH · UniProt Q2T109
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