MolNFT v1 · #40812 · protein
Crystal structure of uridylate kinase from sulfolobus solfataricus in complex with ump and amppcp to 2.1 ångström resolution
2J4J: “Crystal structure of uridylate kinase from sulfolobus solfataricus in complex with ump and amppcp to 2.1…”. X-ray diffraction, 5 ligands (U5P, ACP, 4TC), 16 pockets (best druggability 0.83). MolNFT v1 #40812 on GenesisL1: 3D…
- 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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