MolNFT v1 · #40814 · protein
Crystal structure of uridylate kinase from sulfolobus solfataricus in complex with UTP to 2.8 ångström resolution
2J4L: “Crystal structure of uridylate kinase from sulfolobus solfataricus in complex with UTP to 2.8 ångström…”. X-ray diffraction, 2 ligands (UTP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #40814 on GenesisL1: 3D structure…
- PDB
- 2J4L
- Type
- protein
- Length
- 2,469 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22
- UniProt
- Q97ZE2
- Ligands
- UTP, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 10 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.22) | protein | 214 | 45% helix, 18% strand | Q97ZE2 |
| B, D | Uridylate kinase (EC 2.7.4.22) | protein | 213 | 47% helix, 17% strand | Q97ZE2 |
| C | Uridylate kinase (EC 2.7.4.22) | protein | 198 | 44% helix, 19% strand | Q97ZE2 |
| E | Uridylate kinase (EC 2.7.4.22) | protein | 217 | 48% helix, 17% strand | Q97ZE2 |
| F | Uridylate kinase (EC 2.7.4.22) | protein | 219 | 46% helix, 18% strand | Q97ZE2 |
| G | Uridylate kinase (EC 2.7.4.22) | protein | 212 | 47% helix, 19% strand | Q97ZE2 |
| H | Uridylate kinase (EC 2.7.4.22) | protein | 171 | 47% helix, 18% strand | Q97ZE2 |
| I | Uridylate kinase (EC 2.7.4.22) | protein | 194 | 45% helix, 20% strand | Q97ZE2 |
| J, L | Uridylate kinase (EC 2.7.4.22) | protein | 214 | 46% helix, 19% strand | Q97ZE2 |
| K | Uridylate kinase (EC 2.7.4.22) | protein | 190 | 45% helix, 21% strand | Q97ZE2 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 7 copies · chains B, C, D, E, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.84 | 0.85 | 109 | empty |
| 2 | 1165 | 0.82 | 0.83 | 108 | empty |
| 3 | 365 | 0.77 | 0.87 | 53 | UTP, MG |
| 4 | 640 | 0.75 | 0.81 | 73 | UTP |
| 5 | 433 | 0.71 | 0.82 | 55 | UTP, MG |
Interfaces
27 interfaces between chains.
- A–B · 1467 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1460 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 1424 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 1311 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1297 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2J4L · Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to… · the same entry in another collection · chain L against L, TM-score 1.00
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 2J4L · PDBe 2J4L · UniProt Q97ZE2
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