MolNFT v1 · #109510 · protein + RNA
Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a human menbeta minihelix ending in ccacc
4X4U: “Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a human menbeta minihelix ending in…”. X-ray diffraction, 1 ligand (APC), 20 pockets (best druggability 0.79). MolNFT v1 #109510 on GenesisL1: 3D structure…
- PDB
- 4X4U
- Type
- protein + RNA
- Length
- 1,822 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; Human menbeta minihelix; RNA (5'-D(*GP*G)-3')
- EC
- 2.7.7.72
- UniProt
- O28126
- Ligands
- APC
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.72) | protein | 435 | 40% helix, 22% strand | O28126 |
| B | Human menbeta minihelix | rna | 31 | — | — |
| C, E | Cca-adding enzyme (EC 2.7.7.72) | protein | 437 | 40% helix, 21% strand | O28126 |
| D | Human menbeta minihelix | rna | 26 | — | — |
| F | Cca-adding enzyme (EC 2.7.7.72) | protein | 436 | 44% helix, 23% strand | O28126 |
| G | Human menbeta minihelix | rna | 18 | — | — |
| H | RNA (5'-D(*GP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B, F, G
- GOL · Glycerol · additive · 5 copies · chains A, B, E, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, A, E
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 | 784 | 0.79 | 0.83 | 53 | empty |
| 2 | 869 | 0.79 | 0.81 | 71 | empty |
| 3 | 668 | 0.78 | 0.83 | 44 | APC |
| 4 | 527 | 0.74 | 0.83 | 45 | APC |
| 5 | 739 | 0.74 | 0.80 | 41 | empty |
Interfaces
11 interfaces between chains.
- C–F · 2561 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1523 Ų buried · 33 hydrogen bonds · protein-nucleic
- C–D · 1158 Ų buried · 29 hydrogen bonds · protein-nucleic
- E–F · 1048 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 730 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 4X4U · Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta… · the same entry in another collection · chain G against G, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain A 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 4X4U · PDBe 4X4U · UniProt O28126
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