MolNFT v1 · #107758 · protein
Crystal structure of 3-deoxy-D-manno-octulosonate 8- phosphate phosphatase (kdsc) from moraxella catarrhalis in complex with magnesium ion
4UM7 · 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc: “Crystal structure of 3-deoxy-D-manno-octulosonate 8- phosphate phosphatase (kdsc) from moraxella catarrhalis…”. X-ray diffraction, 1 ligand (MG), 9 pockets (best…
- PDB
- 4UM7
- Type
- protein
- Length
- 696 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
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% 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 | 175 | 44% helix, 19% strand | F1X4B5 |
| B | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc (EC 3.1.3.45) | protein | 173 | 43% helix, 19% strand | F1X4B5 |
| C, D | 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase kdsc (EC 3.1.3.45) | protein | 174 | 44% helix, 19% strand | F1X4B5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
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 | 537 | 0.74 | 0.82 | 81 | empty |
| 2 | 207 | 0.64 | 0.84 | 21 | empty |
| 3 | 218 | 0.62 | 0.82 | 25 | MG |
| 4 | 237 | 0.60 | 0.80 | 22 | MG |
| 5 | 188 | 0.58 | 0.81 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1106 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1078 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1065 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1063 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UM7 · Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (kdsC) 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 F1X4B5
- Elsewhere: RCSB PDB 4UM7 · PDBe 4UM7 · UniProt F1X4B5
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