Research workbench
Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a human menbeta minihelix ending in ccacc and ampcpp
Analyse Crystal structure of the A.FULGIDUS cca-adding enzyme in complex with a human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X4V
- Type
- protein + RNA
- Length
- 933 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cca-adding enzyme; Human menbeta minihelix ending in ccacc
- EC
- 2.7.7.72
- UniProt
- O28126
- Ligands
- 5GP, APC, MG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cca-adding enzyme (EC 2.7.7.72) | protein | 443 | 43% helix, 22% strand | O28126 |
| B | Human menbeta minihelix ending in ccacc | rna | 33 | — | — |
| C | Cca-adding enzyme (EC 2.7.7.72) | protein | 431 | 44% helix, 22% strand | O28126 |
| D | Human menbeta minihelix ending in ccacc | rna | 26 | — | — |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 3 copies · chains B, A, D
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- TAR · D(-)-tartaric acid · additive · 4 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.75 | 0.81 | 60 | APC, MG |
| 2 | 549 | 0.73 | 0.82 | 47 | APC, MG |
| 3 | 809 | 0.72 | 0.77 | 55 | empty |
| 4 | 1013 | 0.71 | 0.75 | 62 | empty |
| 5 | 526 | 0.57 | 0.73 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2575 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1458 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–B · 1432 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 4X4V · Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a human MenBeta… · the same entry in another collection · chain D against D, TM-score 1.00
- O28126 · AlphaFold monomer V2.0 prediction for cca-adding enzyme (O28126) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 4X4V · PDBe 4X4V · UniProt O28126
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