Research workbench
Crystal structure of dimerization module of RNA polymerase I subcomplex A49/A34.5
Analyse Crystal structure of dimerization module of RNA polymerase I subcomplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NFG
- Type
- protein
- Length
- 1,716 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase I subunit RPA49; DNA-directed RNA polymerase I subunit RPA34
- EC
- 2.7.7.6
- UniProt
- Q6FNZ9, Q6FQI3
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I, M, O | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 94 | 6% helix, 57% strand | Q6FNZ9 |
| B, D, F, H, J, L, N | DNA-directed RNA polymerase I subunit RPA34 (EC 2.7.7.6) | protein | 120 | 8% helix, 38% strand | Q6FQI3 |
| C, G, K | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 95 | 6% helix, 56% strand | Q6FNZ9 |
| E | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 96 | 6% helix, 55% strand | Q6FNZ9 |
| P | DNA-directed RNA polymerase I subunit RPA34 (EC 2.7.7.6) | protein | 119 | 8% helix, 38% strand | Q6FQI3 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.83 | 0.84 | 105 | empty |
| 2 | 589 | 0.79 | 0.85 | 63 | empty |
| 3 | 752 | 0.79 | 0.83 | 72 | empty |
| 4 | 1065 | 0.76 | 0.79 | 84 | empty |
| 5 | 693 | 0.73 | 0.79 | 57 | empty |
Interfaces
45 interfaces between chains.
- E–G · 2941 Ų buried · 55 hydrogen bonds · protein-protein
- A–O · 2897 Ų buried · 53 hydrogen bonds · protein-protein
- K–M · 2870 Ų buried · 52 hydrogen bonds · protein-protein
- C–I · 2832 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 1911 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3NFG · Crystal structure of Dimerization module of RNA polymerase I subcomplex A49/A34.5 · 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 Q6FNZ9
- Every structure of UniProt Q6FQI3
- Elsewhere: RCSB PDB 3NFG · PDBe 3NFG · UniProt Q6FNZ9 · UniProt Q6FQI3
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