MolNFT v1 · #40813 · protein
Crystal structure of uridylate kinase from sulfolobus solfataricus in complex with ump to 2.2 ångström resolution
2J4K: “Crystal structure of uridylate kinase from sulfolobus solfataricus in complex with ump to 2.2 ångström…”. X-ray diffraction, 3 ligands (U5P, CD, MG), 20 pockets (best druggability 0.83). MolNFT v1 #40813 on GenesisL1: 3D structure…
- PDB
- 2J4K
- Type
- protein
- Length
- 1,282 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, CD, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.22) | protein | 207 | 42% helix, 19% strand | Q97ZE2 |
| B | Uridylate kinase (EC 2.7.4.22) | protein | 214 | 47% helix, 18% strand | Q97ZE2 |
| C | Uridylate kinase (EC 2.7.4.22) | protein | 206 | 48% helix, 17% strand | Q97ZE2 |
| D | Uridylate kinase (EC 2.7.4.22) | protein | 226 | 47% helix, 17% strand | Q97ZE2 |
| E | Uridylate kinase (EC 2.7.4.22) | protein | 221 | 45% helix, 19% strand | Q97ZE2 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 208 | 47% helix, 18% strand | Q97ZE2 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- CD · Cadmium ion · metal · 18 copies · chains A, C, F, B, D, E
- MG · Magnesium ion · metal · chains A
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 | 881 | 0.83 | 0.85 | 100 | CD |
| 2 | 472 | 0.67 | 0.79 | 54 | U5P |
| 3 | 328 | 0.63 | 0.79 | 34 | U5P |
| 4 | 59 | 0.62 | 0.92 | 17 | empty |
| 5 | 340 | 0.62 | 0.78 | 34 | U5P |
Interfaces
12 interfaces between chains.
- A–B · 1431 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1418 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1396 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1033 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1026 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2J4K · Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP to… · 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 B against A, TM-score 0.98
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 2J4K · PDBe 2J4K · UniProt Q97ZE2
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