Research workbench
Metal rok rebel: characterisation of N-acetylmannosamine kinase from the pathogen staphylococcus aureus
Analyse Metal rok rebel: characterisation of N-acetylmannosamine kinase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q28
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylmannosamine kinase
- EC
- 2.7.1.2, 2.7.1.85
- UniProt
- A0A266CX40
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acetylmannosamine kinase (EC 2.7.1.2, 2.7.1.85) | protein | 286 | 38% helix, 21% strand | A0A266CX40 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.79 | 0.84 | 79 | NAG |
| 2 | 1153 | 0.78 | 0.80 | 113 | NAG |
| 3 | 857 | 0.78 | 0.81 | 89 | NAG |
| 4 | 744 | 0.77 | 0.82 | 77 | NAG |
| 5 | 58 | 0.72 | 0.99 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1761 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 804 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 795 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6Q28 · Metal ROK rebel: Characterisation of N-acetylmannosamine kinase from the pathogen… · 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 A0A266CX40
- Elsewhere: RCSB PDB 6Q28 · PDBe 6Q28 · UniProt A0A266CX40
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