MolNFT v1 · #168341 · protein
Crystal structure of a guanylate kinase from stenotrophomonas maltophilia K279A bound to guanosine-5'-monophosphate
6WCT: “Crystal structure of a guanylate kinase from stenotrophomonas maltophilia K279A bound to…”. X-ray diffraction, 2 ligands (5GP, PO4), 16 pockets (best druggability 0.75). MolNFT v1 #168341 on GenesisL1: 3D structure, binding sites…
- PDB
- 6WCT
- Type
- protein
- Length
- 808 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- B2FT06
- Ligands
- 5GP, PO4
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 204 | 47% helix, 21% strand | B2FT06 |
| B | Guanylate kinase (EC 2.7.4.8) | protein | 198 | 46% helix, 21% strand | B2FT06 |
| C | Guanylate kinase (EC 2.7.4.8) | protein | 199 | 48% helix, 20% strand | B2FT06 |
| D | Guanylate kinase (EC 2.7.4.8) | protein | 207 | 47% helix, 20% strand | B2FT06 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.75 | 0.85 | 48 | 5GP, PO4 |
| 2 | 312 | 0.63 | 0.80 | 35 | 5GP |
| 3 | 460 | 0.63 | 0.76 | 44 | 5GP |
| 4 | 333 | 0.62 | 0.79 | 40 | 5GP |
| 5 | 394 | 0.55 | 0.74 | 38 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1638 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1618 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 151 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 122 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6WCT · Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a bound to… · 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 B2FT06
- Elsewhere: RCSB PDB 6WCT · PDBe 6WCT · UniProt B2FT06
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