MolNFT v1 · #101999 · protein + RNA
Crystal structure of rtca, the RNA 3'-terminal phosphate cyclase from pyrococcus horikoshii, in complex with RACAAA3'PHOSPHATE and adenine.
4O8J: “Crystal structure of rtca, the RNA 3'-terminal phosphate cyclase from pyrococcus horikoshii, in complex with…”. X-ray diffraction, 1 ligand (ADN), 5 pockets (best druggability 0.64). MolNFT v1 #101999 on GenesisL1: 3D structure…
- PDB
- 4O8J
- Type
- protein + RNA
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 3'-terminal phosphate cyclase; RNA
- EC
- 6.5.1.4
- UniProt
- O59198
- Ligands
- ADN
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA 3'-terminal phosphate cyclase (EC 6.5.1.4) | protein | 341 | 34% helix, 29% strand | O59198 |
| D, E | RNA | rna | 5 | — | — |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, E, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.64 | 0.76 | 48 | empty |
| 2 | 261 | 0.59 | 0.79 | 29 | ADN |
| 3 | 246 | 0.56 | 0.78 | 28 | ADN |
| 4 | 135 | 0.44 | 0.76 | 23 | empty |
| 5 | 119 | 0.41 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–D · 694 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 684 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 441 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4O8J · Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- O59198 · AlphaFold monomer V2.0 prediction for RNA 3'-terminal phosphate cyclase (O59198) · a predicted model of the same protein · chain A against A, 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 O59198
- Elsewhere: RCSB PDB 4O8J · PDBe 4O8J · UniProt O59198
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