Research workbench
RNA polymerase II binary complex with DNA
Analyse RNA polymerase II binary complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A3I
- Type
- protein + DNA
- Length
- 3,955 residues
- Chains
- 14
- 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
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 14 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1422 | 41% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1115 | 29% helix, 25% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 25% helix, 26% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 49% helix, 6% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1 | protein | 214 | 36% helix, 24% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2 | protein | 84 | 35% helix, 15% strand | P20435 |
| G | RPB7, DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 50% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3 | protein | 133 | 2% helix, 44% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 4% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5 | protein | 65 | 46% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 36% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4 | protein | 46 | 0% helix, 13% strand | P40422 |
| N | 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*GP*CP*T)-3' | dna | 11 | — | — |
| T | Template DNA 27-mer | dna | 17 | — | — |
Ligands and binding sites
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 | 1005 | 0.89 | 0.90 | 112 | empty |
| 2 | 1197 | 0.84 | 0.86 | 119 | empty |
| 3 | 909 | 0.80 | 0.83 | 94 | empty |
| 4 | 632 | 0.80 | 0.85 | 62 | empty |
| 5 | 147 | 0.80 | 0.97 | 36 | empty |
Interfaces
32 interfaces between chains.
- A–B · 9670 Ų buried · 156 hydrogen bonds · protein-protein
- D–G · 2459 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 2250 Ų buried · 35 hydrogen bonds · protein-protein
- C–K · 2185 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 2087 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4A3I · RNA Polymerase II binary complex with DNA · 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 P20433
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- 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 4A3I · PDBe 4A3I · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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