MolNFT v1 · #186634 · protein
Yeast CTP synthase (URA8) tetramer bound to ATP/UTP at neutral pH
7RKH: “Yeast CTP synthase (URA8) tetramer bound to ATP/UTP at neutral pH”. Electron microscopy, 3 ligands (UTP, ATP, MG), 19 pockets (best druggability 0.88). MolNFT v1 #186634 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RKH
- Type
- protein
- Length
- 2,236 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTP synthase
- EC
- 6.3.4.2
- UniProt
- A0A6A5PYW3
- Ligands
- UTP, ATP, MG
- Pockets
- 19 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C | CTP synthase (EC 6.3.4.2) | protein | 559 | 45% helix, 21% strand | A0A6A5PYW3 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 4 copies · chains D, B, C, A
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains D, C, A, B
- MG · Magnesium ion · metal · 8 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.88 | 0.90 | 145 | UTP, ATP, MG |
| 2 | 579 | 0.84 | 0.90 | 89 | MG, UTP, ATP |
| 3 | 422 | 0.82 | 0.90 | 72 | UTP, ATP, MG |
| 4 | 254 | 0.67 | 0.83 | 41 | empty |
| 5 | 234 | 0.66 | 0.84 | 42 | empty |
Interfaces
6 interfaces between chains.
- D–B · 1419 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1417 Ų buried · 22 hydrogen bonds · protein-protein
- D–C · 766 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 763 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 538 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RKH · Yeast CTP Synthase (URA8) tetramer bound to ATP/UTP at neutral pH · the same entry in another collection · chain D against D, 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 A0A6A5PYW3
- Elsewhere: RCSB PDB 7RKH · PDBe 7RKH · UniProt A0A6A5PYW3
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