MolNFT v1 · #109505 · protein + RNA
Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in ccac
4X4P: “Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #109505 on GenesisL1: 3D structure…
- PDB
- 4X4P
- Type
- protein + RNA
- Length
- 1,848 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; G70A tRNA minihelix ending in ccac
- EC
- 2.7.7.72
- UniProt
- O28126
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.72) | protein | 437 | 44% helix, 21% strand | O28126 |
| B | G70A tRNA minihelix ending in ccac | rna | 36 | — | — |
| C | Cca-adding enzyme (EC 2.7.7.72) | protein | 434 | 42% helix, 21% strand | O28126 |
| D | G70A tRNA minihelix ending in ccac | rna | 30 | — | — |
| E | Cca-adding enzyme (EC 2.7.7.72) | protein | 428 | 44% helix, 20% strand | O28126 |
| F | G70A tRNA minihelix ending in ccac | rna | 27 | — | — |
| G | Cca-adding enzyme (EC 2.7.7.72) | protein | 428 | 44% helix, 21% strand | O28126 |
| H | G70A tRNA minihelix ending in ccac | rna | 28 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.81 | 0.87 | 56 | SO4 |
| 2 | 747 | 0.77 | 0.82 | 50 | SO4 |
| 3 | 829 | 0.77 | 0.81 | 55 | SO4 |
| 4 | 702 | 0.76 | 0.81 | 39 | SO4 |
| 5 | 787 | 0.71 | 0.77 | 50 | empty |
Interfaces
7 interfaces between chains.
- A–C · 2543 Ų buried · 48 hydrogen bonds · protein-protein
- E–G · 2502 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 30 hydrogen bonds · protein-nucleic
- G–H · 1214 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 1207 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 4X4P · Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA… · the same entry in another collection · chain H against H, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 O28126
- Elsewhere: RCSB PDB 4X4P · PDBe 4X4P · UniProt O28126
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