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Unique GTP-binding pocket and allostery of ump kinase from a gram- negative phytopathogen bacterium
Analyse Unique GTP-binding pocket and allostery of ump kinase from a gram- negative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EK6
- Type
- protein
- Length
- 1,436 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
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.22) | protein | 243 | 39% helix, 17% strand | P59009 |
| B, D | Uridylate kinase (EC 2.7.4.22) | protein | 240 | 36% helix, 18% strand | P59009 |
| C, F | Uridylate kinase (EC 2.7.4.22) | protein | 238 | 36% helix, 18% strand | P59009 |
| E | Uridylate kinase (EC 2.7.4.22) | protein | 237 | 37% helix, 17% strand | P59009 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.82 | 0.90 | 57 | empty |
| 2 | 243 | 0.80 | 0.93 | 36 | empty |
| 3 | 214 | 0.78 | 0.93 | 33 | empty |
| 4 | 187 | 0.78 | 0.94 | 34 | empty |
| 5 | 302 | 0.78 | 0.90 | 43 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1355 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1343 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1314 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 838 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 803 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3EK6 · 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 E 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 3EK6 · PDBe 3EK6 · UniProt P59009
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