MolNFT v1 · #19512 · protein
Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology
1QMH: “Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology”. X-ray diffraction, 1 ligand (DTO), 4 pockets (best druggability 0.77). MolNFT v1 #19512 on GenesisL1: 3D structure, binding sites…
- PDB
- 1QMH
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 3'-terminal phosphate cyclase
- EC
- 6.5.1.4
- UniProt
- P46849
- Ligands
- DTO
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 334 | 34% helix, 32% strand | P46849 |
| B | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 335 | 34% helix, 32% strand | P46849 |
Ligands and binding sites
- DTO · 1-hydroxysulfanyl-4-mercapto-butane-2,3-diol · ligand · chains B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.77 | 0.79 | 95 | CIT |
| 2 | 1001 | 0.76 | 0.79 | 94 | CIT |
| 3 | 77 | 0.36 | 0.76 | 21 | empty |
| 4 | 80 | 0.34 | 0.74 | 20 | DTO |
Interfaces
1 interface between chains.
- A–B · 739 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1QMH · Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual… · the same entry in another collection · chain A against A, TM-score 1.00
- P46849 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase (P46849) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P46849
- Elsewhere: RCSB PDB 1QMH · PDBe 1QMH · UniProt P46849
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