MolNFT v1 · #62594 · protein
Unique GTP-binding pocket and allostery of ump kinase from a gram- negative phytopathogen bacterium
3EK5 · Uridylate kinase: “Unique GTP-binding pocket and allostery of ump kinase from a gram- negative phytopathogen bacterium”. X-ray diffraction, 1 ligand (GTP), 20 pockets (best druggability 0.88). MolNFT v1 #62594 on GenesisL1: 3D…
- PDB
- 3EK5
- Type
- protein
- Length
- 1,435 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- P59009
- Ligands
- GTP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.22) | protein | 241 | 38% helix, 17% strand | P59009 |
| B, C, D, E | Uridylate kinase (EC 2.7.4.22) | protein | 239 | 35% helix, 17% strand | P59009 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 238 | 39% helix, 14% strand | P59009 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains B, C, F, A, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.88 | 0.89 | 136 | GTP |
| 2 | 387 | 0.81 | 0.90 | 64 | GTP |
| 3 | 390 | 0.60 | 0.77 | 62 | empty |
| 4 | 225 | 0.55 | 0.79 | 38 | empty |
| 5 | 187 | 0.55 | 0.80 | 37 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1354 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1327 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1313 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 841 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 837 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3EK5 · Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen… · the same entry in another collection · chain F against F, TM-score 1.00
- P59009 · AlphaFold monomer V2.0 prediction for uridylate kinase (P59009) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P59009
- Elsewhere: RCSB PDB 3EK5 · PDBe 3EK5 · UniProt P59009
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