MolNFT v1 · #120815 · protein + RNA
Thermotoga maritima cca-adding enzyme complexed with TRNA_CCA
5HC9 · TRNA nucleotidyl transferase-related protein: “Thermotoga maritima cca-adding enzyme complexed with TRNA_CCA”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.80). MolNFT v1 #120815 on GenesisL1: 3D structure…
- PDB
- 5HC9
- Type
- protein + RNA
- Length
- 987 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA nucleotidyl transferase-related protein; Trnaphe
- EC
- 2.7.7.72
- UniProt
- Q9WZH4
- Ligands
- MG
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA nucleotidyl transferase-related protein (EC 2.7.7.72) | protein | 425 | 57% helix, 10% strand | Q9WZH4 |
| B | TRNA nucleotidyl transferase-related protein (EC 2.7.7.72) | protein | 410 | 58% helix, 10% strand | Q9WZH4 |
| C, D | Trnaphe | rna | 76 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.80 | 0.84 | 63 | empty |
| 2 | 537 | 0.71 | 0.81 | 55 | MG |
| 3 | 716 | 0.71 | 0.79 | 34 | empty |
| 4 | 701 | 0.70 | 0.79 | 36 | empty |
| 5 | 561 | 0.70 | 0.80 | 53 | MG |
Interfaces
3 interfaces between chains.
- A–C · 1396 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–D · 1373 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 525 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5HC9 · Thermotoga maritima CCA-adding enzyme complexed with tRNA_CCA · the same entry in another collection · 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 Q9WZH4
- Elsewhere: RCSB PDB 5HC9 · PDBe 5HC9 · UniProt Q9WZH4
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