Research workbench
Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from moraxella catarrhalis in complex with magnesium ion, phosphate ion and kdo molecule
Analyse Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UMF
- Type
- protein
- Length
- 693 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc
- EC
- 3.1.3.45
- UniProt
- F1X4B5
- Ligands
- KDO, MG, PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc (EC 3.1.3.45) | protein | 173 | 43% helix, 19% strand | F1X4B5 |
| C | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc (EC 3.1.3.45) | protein | 174 | 42% helix, 21% strand | F1X4B5 |
Ligands and binding sites
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.72 | 0.80 | 81 | PO4 |
| 2 | 168 | 0.64 | 0.85 | 21 | PO4, MG, KDO |
| 3 | 238 | 0.62 | 0.81 | 27 | KDO, PO4, MG |
| 4 | 213 | 0.62 | 0.82 | 25 | PO4, MG, KDO |
| 5 | 146 | 0.61 | 0.85 | 19 | KDO, PO4, MG |
Interfaces
6 interfaces between chains.
- C–D · 1147 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1109 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1077 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1052 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UMF · Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella… · 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 F1X4B5
- Elsewhere: RCSB PDB 4UMF · PDBe 4UMF · UniProt F1X4B5
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