MolNFT v1 · #15892 · protein
Wild type RNA polymerase II
1NIK · RPB1: “Wild type RNA polymerase II”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.88). MolNFT v1 #15892 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NIK
- Type
- protein
- Length
- 3,849 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RPB1; Orf YOR151C; DNA-directed RNA polymerase II, chain RPB3; DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 12 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RPB1 (EC 2.7.7.6) | protein | 1388 | 39% helix, 15% strand | P04050 |
| B | Orf YOR151C (EC 2.7.7.6) | protein | 1097 | 28% helix, 22% strand | P08518 |
| C | DNA-directed RNA polymerase II, chain RPB3 (EC 2.7.7.6) | protein | 266 | 26% helix, 23% strand | P16370 |
| D | DNA-directed RNA polymerase II, chain RPB4 (EC 2.7.7.6) | protein | 153 | 0% helix, 0% strand | — |
| E | DNA-directed RNA polymerase II, chain RPB5 (EC 2.7.7.6) | protein | 214 | 36% helix, 21% strand | P20434 |
| F | DNA-directed RNA polymerase I, II and III 23 kda polypeptide (EC 2.7.7.6) | protein | 84 | 30% helix, 14% strand | P20435 |
| G | DNA-directed RNA polymerase II, chain RPB7 (EC 2.7.7.6) | protein | 170 | 0% helix, 0% strand | — |
| H | DNA-directed RNA polymerase subunit RPB8 (EC 2.7.7.6) | protein | 133 | 5% helix, 43% strand | P20436 |
| I | DNA-directed RNA polymerase II, chain RPB9 (EC 2.7.7.6) | protein | 119 | 4% helix, 27% strand | P27999 |
| J | DNA-directed RNA polymerase II, chain RPB10 (EC 2.7.7.6) | protein | 65 | 43% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II, chain RPB11 (EC 2.7.7.6) | protein | 114 | 38% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerase II, chain RPB12 (EC 2.7.7.6) | protein | 46 | 0% helix, 9% strand | P40422 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, C, I, J
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 | 1004 | 0.88 | 0.90 | 121 | empty |
| 2 | 795 | 0.85 | 0.88 | 88 | empty |
| 3 | 753 | 0.81 | 0.85 | 88 | empty |
| 4 | 656 | 0.80 | 0.85 | 65 | empty |
| 5 | 1031 | 0.80 | 0.82 | 95 | empty |
Interfaces
28 interfaces between chains.
- A–B · 9439 Ų buried · 143 hydrogen bonds · protein-protein
- A–E · 2200 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 2138 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1845 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1786 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 1NIK · Wild Type RNA Polymerase II · 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 P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P20436
- Every structure of UniProt P27999
- Every structure of UniProt P22139
- Every structure of UniProt P38902
- Every structure of UniProt P40422
- Elsewhere: RCSB PDB 1NIK · PDBe 1NIK · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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