MolNFT v1 · #32868 · protein
Subunits RPB4 and RPB7 of human RNA polymerase II
2C35 · DNA-directed RNA polymerase II 16 kda polypeptide: “Subunits RPB4 and RPB7 of human RNA polymerase II”. X-ray diffraction, 10 pockets (best druggability 0.52). MolNFT v1 #32868 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2C35
- Type
- protein
- Length
- 1,192 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II 16 kda polypeptide; DNA-directed RNA polymerase II 19 kda…
- EC
- 2.7.7.6
- UniProt
- O15514, P62487
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA-directed RNA polymerase II 16 kda polypeptide (EC 2.7.7.6) | protein | 128 | 60% helix, 3% strand | O15514 |
| B, D, F, H | DNA-directed RNA polymerase II 19 kda polypeptide | protein | 171 | 11% helix, 54% strand | P62487 |
| E, G | DNA-directed RNA polymerase II 16 kda polypeptide (EC 2.7.7.6) | protein | 126 | 63% helix, 4% strand | O15514 |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.52 | 0.75 | 31 | empty |
| 2 | 161 | 0.47 | 0.77 | 23 | empty |
| 3 | 158 | 0.46 | 0.76 | 24 | empty |
| 4 | 105 | 0.40 | 0.76 | 23 | empty |
| 5 | 74 | 0.34 | 0.76 | 16 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1829 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1826 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1767 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1758 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 900 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2C35 · Subunits Rpb4 and Rpb7 of human RNA polymerase II · the same entry in another collection · chain H against H, TM-score 1.00
- P62487 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB7 (P62487) · a predicted model of the same protein · chain B against A, TM-score 0.95
- O15514 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB4 (O15514) · a predicted model of the same protein · chain E against A, TM-score 0.95
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 O15514
- Every structure of UniProt P62487
- Elsewhere: RCSB PDB 2C35 · PDBe 2C35 · UniProt O15514 · UniProt P62487
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