MolNFT v1 · #27636 · protein
Crystal structure of TA1416,DNA-directed RNA polymerase subunit L, from thermoplasma acidophilum
1XPP: “Crystal structure of TA1416,DNA-directed RNA polymerase subunit L, from thermoplasma acidophilum”. X-ray diffraction, 1 ligand (SCN), 3 pockets (best druggability 0.61). MolNFT v1 #27636 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1XPP
- Type
- protein
- Length
- 397 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit L
- EC
- 2.7.7.6
- UniProt
- Q9HIC5
- Ligands
- SCN
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 99 | 44% helix, 27% strand | Q9HIC5 |
| B | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 98 | 45% helix, 29% strand | Q9HIC5 |
| D | DNA-directed RNA polymerase subunit L (EC 2.7.7.6) | protein | 101 | 43% helix, 28% strand | Q9HIC5 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B, C, D
- ACY · Acetic acid · additive · chains A, B
- FMT · Formic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.61 | 0.81 | 39 | empty |
| 2 | 127 | 0.44 | 0.77 | 25 | empty |
| 3 | 54 | 0.38 | 0.80 | 15 | SCN |
Interfaces
6 interfaces between chains.
- C–D · 1923 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1808 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 304 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 214 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 170 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1XPP · Crystal Structure of TA1416,DNA-directed RNA polymerase subunit L, from Thermoplasma… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HIC5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit L (Q9HIC5) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q9HIC5
- Elsewhere: RCSB PDB 1XPP · PDBe 1XPP · UniProt Q9HIC5
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