Research workbench
Crystal structure of N-acetyl mannosmaine kinase with AMP-PNP from Pasteurella multocida
Analyse Crystal structure of N-acetyl mannosmaine kinase with AMP-PNP from Pasteurella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JDO
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.002
- Source
- Pasteurella multocida
- Molecule
- N-acetylmannosamine kinase
- EC
- 2.7.1.60
- UniProt
- A0A2K0XYW4
- Ligands
- ANP, CA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.002 · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylmannosamine kinase (EC 2.7.1.60) | protein | 293 | 39% helix, 24% strand | A0A2K0XYW4 |
| B | N-acetylmannosamine kinase (EC 2.7.1.60) | protein | 291 | 39% helix, 24% strand | A0A2K0XYW4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.76 | 0.98 | 16 | empty |
| 2 | 474 | 0.63 | 0.76 | 48 | empty |
| 3 | 504 | 0.62 | 0.75 | 57 | empty |
| 4 | 142 | 0.44 | 0.76 | 29 | empty |
| 5 | 131 | 0.43 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1632 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6JDO · Crystal structure of N-acetyl mannosmaine kinase with AMP-pnp from pasteurella multocida · 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 A0A2K0XYW4
- Elsewhere: RCSB PDB 6JDO · PDBe 6JDO · UniProt A0A2K0XYW4
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