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Crystal structure of uridylate kinase from sulfolobus solfataricus in complex with ump and amppcp to 2.1 ångström resolution
Analyse Crystal structure of uridylate kinase from sulfolobus solfataricus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J4J
- Type
- protein
- Length
- 1,305 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- Q97ZE2
- Ligands
- U5P, ACP, 4TC, CO, MG
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Uridylate kinase (EC 2.7.4.22) | protein | 216 | 48% helix, 18% strand | Q97ZE2 |
| C | Uridylate kinase (EC 2.7.4.22) | protein | 215 | 49% helix, 19% strand | Q97ZE2 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 226 | 47% helix, 18% strand | Q97ZE2 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 5 copies · chains A, B, C, D, E
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 5 copies · chains A, B, C, D, E
- 4TC · P1-(5'-adenosine)p4-(5'-uridine)-beta,gamma-methylene tetraphosphate · ligand · chains F
- CO · Cobalt (II) ion · metal · 6 copies · chains A, C, E, B, D, F
- MG · Magnesium ion · metal · 2 copies · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.83 | 0.85 | 109 | CO |
| 2 | 355 | 0.77 | 0.88 | 58 | 4TC, MG |
| 3 | 459 | 0.68 | 0.80 | 52 | U5P, ACP, MG |
| 4 | 459 | 0.68 | 0.80 | 48 | U5P, ACP, CO |
| 5 | 388 | 0.68 | 0.81 | 53 | U5P, ACP, CO |
Interfaces
12 interfaces between chains.
- A–B · 1508 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1485 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1480 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 1117 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1035 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2J4J · Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP… · the same entry in another collection · chain F against F, TM-score 1.00
- Q97ZE2 · AlphaFold monomer V2.0 prediction for uridylate kinase (Q97ZE2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q97ZE2
- Elsewhere: RCSB PDB 2J4J · PDBe 2J4J · UniProt Q97ZE2
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