Research workbench
D-glycerate 3-kinase from cryptococcus neoformans var. grubii serotype a (H99 / atcc 208821 / cbs 10515 / fgsc 9487)
Analyse D-glycerate 3-kinase from cryptococcus neoformans var. grubii serotype a (H99 /… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CKG
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glycerate 3-kinase
- EC
- 2.7.1.31
- UniProt
- J9VS00
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-glycerate 3-kinase (EC 2.7.1.31) | protein | 292 | 47% helix, 19% strand | J9VS00 |
| B | D-glycerate 3-kinase (EC 2.7.1.31) | protein | 290 | 46% helix, 19% strand | J9VS00 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.71 | 0.75 | 107 | EDO |
| 2 | 463 | 0.64 | 0.77 | 50 | EDO |
| 3 | 89 | 0.31 | 0.72 | 19 | empty |
| 4 | 74 | 0.29 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 210 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6CKG · D-glycerate 3-kinase from Cryptococcus neoformans var. grubii serotype A (H99 / ATCC… · 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 J9VS00
- Elsewhere: RCSB PDB 6CKG · PDBe 6CKG · UniProt J9VS00
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