Research workbench
Kina pas-a domain, homodimer
Analyse Kina pas-a domain, homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VLG
- Type
- protein
- Length
- 389 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sporulation kinase a
- EC
- 2.7.13.3
- UniProt
- P16497
- Ligands
- CL
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sporulation kinase a (EC 2.7.13.3) | protein | 93 | 27% helix, 38% strand | P16497 |
| B | Sporulation kinase a (EC 2.7.13.3) | protein | 93 | 27% helix, 38% strand | P16497 |
| C | Sporulation kinase a (EC 2.7.13.3) | protein | 102 | 22% helix, 43% strand | P16497 |
| D | Sporulation kinase a (EC 2.7.13.3) | protein | 101 | 23% helix, 44% strand | P16497 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.62 | 0.78 | 51 | CL |
| 2 | 228 | 0.59 | 0.79 | 39 | CL |
| 3 | 168 | 0.50 | 0.78 | 24 | empty |
| 4 | 127 | 0.48 | 0.79 | 17 | empty |
| 5 | 51 | 0.28 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 828 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 791 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 P16497
- Elsewhere: RCSB PDB 2VLG · PDBe 2VLG · UniProt P16497
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