MolNFT v1 · #153408 · protein
Crystal structure of N-acetyl mannosmaine kinase from pasteurella multocida
6JDH · N-acetylmannosamine kinase: “Crystal structure of N-acetyl mannosmaine kinase from pasteurella multocida”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.75). MolNFT v1 #153408 on GenesisL1: 3D structure, binding…
- PDB
- 6JDH
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylmannosamine kinase
- EC
- 2.7.1.60
- UniProt
- A0A2K0XYW4
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylmannosamine kinase (EC 2.7.1.60) | protein | 293 | 41% helix, 24% strand | A0A2K0XYW4 |
| B | N-acetylmannosamine kinase (EC 2.7.1.60) | protein | 291 | 41% helix, 24% strand | A0A2K0XYW4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.75 | 0.98 | 16 | empty |
| 2 | 553 | 0.65 | 0.76 | 60 | empty |
| 3 | 535 | 0.64 | 0.76 | 56 | empty |
| 4 | 157 | 0.46 | 0.76 | 26 | empty |
| 5 | 156 | 0.45 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1618 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6JDH · Crystal structure of N-acetyl mannosmaine kinase 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 6JDH · PDBe 6JDH · UniProt A0A2K0XYW4
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