Research workbench
Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from moraxella catarrhalis in complex with magnesium ion and phosphate ion
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
- 4UM5
- Type
- protein
- Length
- 691 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
- MG, PO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc (EC 3.1.3.45) | protein | 172 | 43% helix, 19% strand | F1X4B5 |
| B, C, D | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc (EC 3.1.3.45) | protein | 173 | 42% helix, 20% strand | F1X4B5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.73 | 0.80 | 64 | EDO |
| 2 | 204 | 0.63 | 0.83 | 24 | MG, PO4 |
| 3 | 292 | 0.62 | 0.80 | 29 | MG, PO4 |
| 4 | 171 | 0.62 | 0.84 | 20 | PO4 |
| 5 | 194 | 0.61 | 0.82 | 23 | MG, PO4 |
Interfaces
6 interfaces between chains.
- C–D · 1121 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1091 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1081 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1044 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UM5 · 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 4UM5 · PDBe 4UM5 · UniProt F1X4B5
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