MolNFT v1 · #65556 · protein
RNA polymerase II from schizosaccharomyces pombe
3H0G · DNA-directed RNA polymerase II subunit RPB1: “RNA polymerase II from schizosaccharomyces pombe”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #65556 on GenesisL1: 3D structure, binding sites…
- PDB
- 3H0G
- Type
- protein
- Length
- 7,904 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
- EC
- 2.7.7.6
- UniProt
- P36594, Q02061, P37382, O74825, Q09191, P36595, O14459, Q92399, O74635, O13877, P87123, P48011
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 13 distinct chains · 26% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1496 | 30% helix, 9% strand | P36594 |
| B, N | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1150 | 21% helix, 11% strand | Q02061 |
| C, O | DNA-directed RNA polymerase II subunit RPB3 | protein | 263 | 20% helix, 21% strand | P37382 |
| D, P | DNA-directed RNA polymerase II subunit RPB4 | protein | 130 | 57% helix, 1% strand | O74825 |
| E, Q | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 207 | 22% helix, 14% strand | Q09191 |
| F, R | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 83 | 29% helix, 7% strand | P36595 |
| G, S | DNA-directed RNA polymerase II subunit RPB7 | protein | 170 | 11% helix, 43% strand | O14459 |
| H, T | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 124 | 3% helix, 24% strand | Q92399 |
| I, U | DNA-directed RNA polymerase II subunit RPB9 | protein | 111 | 0% helix, 17% strand | O74635 |
| J, V | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 64 | 31% helix, 2% strand | O13877 |
| K, W | DNA-directed RNA polymerase II subunit RPB11 | protein | 119 | 32% helix, 16% strand | P87123 |
| L, X | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 13% strand | P48011 |
| M | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1476 | 31% helix, 9% strand | P36594 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, I, J, L, M, N, O, U, V, X
- MG · Magnesium ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.86 | 0.87 | 140 | empty |
| 2 | 745 | 0.85 | 0.89 | 80 | empty |
| 3 | 804 | 0.85 | 0.88 | 86 | empty |
| 4 | 783 | 0.83 | 0.86 | 90 | empty |
| 5 | 617 | 0.83 | 0.88 | 85 | empty |
Interfaces
60 interfaces between chains.
- A–B · 9930 Ų buried · 133 hydrogen bonds · protein-protein
- M–N · 9891 Ų buried · 130 hydrogen bonds · protein-protein
- M–Q · 2333 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 2323 Ų buried · 34 hydrogen bonds · protein-protein
- A–F · 2173 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3H0G · RNA Polymerase II from Schizosaccharomyces pombe · the same entry in another collection · chain K against K, 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 P36594
- Every structure of UniProt Q02061
- Every structure of UniProt P37382
- Every structure of UniProt O74825
- Every structure of UniProt Q09191
- Every structure of UniProt P36595
- Every structure of UniProt O14459
- Every structure of UniProt Q92399
- Every structure of UniProt O74635
- Every structure of UniProt O13877
- Every structure of UniProt P87123
- Every structure of UniProt P48011
- Elsewhere: RCSB PDB 3H0G · PDBe 3H0G · UniProt P36594 · UniProt Q02061 · UniProt P37382 · UniProt O74825 · UniProt Q09191 · UniProt P36595 · UniProt O14459 · UniProt Q92399 · UniProt O74635 · UniProt O13877 · UniProt P87123 · UniProt P48011
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.