MolNFT v1 · #109503 · protein + RNA
Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix
4X4N: “Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a G70A arginyl-tRNA minihelix”. X-ray diffraction, 3 ligands (GMP, 5GP, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #109503 on GenesisL1: 3D structure…
- PDB
- 4X4N
- Type
- protein + RNA
- Length
- 1,830 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; G70A tRNA minihelix; RNA (5'-D(P*CP*G)-3')
- EC
- 2.7.7.72
- UniProt
- O28126
- Ligands
- GMP, 5GP, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Cca-adding enzyme (EC 2.7.7.72) | protein | 437 | 42% helix, 21% strand | O28126 |
| G | G70A tRNA minihelix | rna | 18 | — | — |
| B | G70A tRNA minihelix | rna | 32 | — | — |
| C | Cca-adding enzyme (EC 2.7.7.72) | protein | 436 | 43% helix, 21% strand | O28126 |
| D | G70A tRNA minihelix | rna | 31 | — | — |
| I | RNA (5'-D(P*CP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- GMP · Guanosine · ligand · chains A, B
- 5GP · Guanosine-5'-monophosphate · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, E, F
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.80 | 0.82 | 70 | SO4 |
| 2 | 681 | 0.79 | 0.84 | 49 | SO4 |
| 3 | 1077 | 0.78 | 0.80 | 83 | empty |
| 4 | 814 | 0.77 | 0.81 | 53 | SO4 |
| 5 | 605 | 0.74 | 0.81 | 45 | SO4 |
Interfaces
12 interfaces between chains.
- C–F · 2619 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 1262 Ų buried · 34 hydrogen bonds · protein-nucleic
- C–D · 1225 Ų buried · 28 hydrogen bonds · protein-nucleic
- E–F · 1068 Ų buried · 13 hydrogen bonds · protein-protein
- G–F · 734 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain C 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 4X4N · PDBe 4X4N · UniProt O28126
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