MolNFT v1 · #156803 · protein
Crystal structure of a guanylate kinase from cryptococcus neoformans var. grubii serotype a in complex with GDP and ADP
6MFU: “Crystal structure of a guanylate kinase from cryptococcus neoformans var. grubii serotype a in complex with…”. X-ray diffraction, 2 ligands (5GP, ADP), 13 pockets (best druggability 0.70). MolNFT v1 #156803 on GenesisL1: 3D…
- PDB
- 6MFU
- Type
- protein
- Length
- 862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- UniProt
- J9VQ84
- Ligands
- 5GP, ADP
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Guanylate kinase | protein | 216 | 42% helix, 19% strand | J9VQ84 |
| B, D | Guanylate kinase | protein | 215 | 42% helix, 20% strand | J9VQ84 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.70 | 0.83 | 42 | 5GP, ADP |
| 2 | 285 | 0.70 | 0.85 | 41 | 5GP, ADP |
| 3 | 300 | 0.70 | 0.84 | 43 | 5GP, ADP |
| 4 | 289 | 0.69 | 0.84 | 43 | 5GP, ADP |
| 5 | 426 | 0.62 | 0.77 | 38 | empty |
Interfaces
3 interfaces between chains.
- B–C · 830 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 826 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6MFU · Crystal structure of a Guanylate kinase from Cryptococcus neoformans var. grubii serotype… · 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 J9VQ84
- Elsewhere: RCSB PDB 6MFU · PDBe 6MFU · UniProt J9VQ84
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.