MolNFT v1 · #10964 · protein
Structure of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (yrbi) from haemophilus influenzae (HI1679)
1J8D: “Structure of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (yrbi) from…”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #10964 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1J8D
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxy-D-mannose-octulosonate 8-phosphate phosphatase
- EC
- 3.1.3.-
- UniProt
- P45314
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Deoxy-D-mannose-octulosonate 8-phosphate phosphatase (EC 3.1.3.-) | protein | 180 | 44% helix, 20% strand | P45314 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.72 | 0.81 | 64 | GOL |
| 2 | 80 | 0.65 | 0.92 | 18 | empty |
| 3 | 70 | 0.65 | 0.93 | 17 | empty |
| 4 | 63 | 0.65 | 0.94 | 18 | empty |
| 5 | 148 | 0.43 | 0.75 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1169 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1149 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1141 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1136 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 1J8D · Structure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P45314 · AlphaFold monomer V2.0 prediction for 3-deoxy-D-manno-octulosonate 8-phosphate… · 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 P45314
- Elsewhere: RCSB PDB 1J8D · PDBe 1J8D · UniProt P45314
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