Research workbench
RNA polymerase II initial transcribing complex with a 5NT DNA-RNA hybrid and soaked with ampcpp
Analyse RNA polymerase II initial transcribing complex with a 5NT DNA-RNA hybrid and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A3E
- Type
- protein + DNA + RNA
- Length
- 3,958 residues
- Chains
- 15
- 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
- APC, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 15 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1423 | 41% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1115 | 28% helix, 24% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 26% helix, 27% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 53% helix, 5% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1 | protein | 214 | 39% helix, 22% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2 | protein | 84 | 31% helix, 15% strand | P20435 |
| G | RPB7, DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 13% helix, 50% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3 | protein | 133 | 2% helix, 45% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 3% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5 | protein | 65 | 45% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 39% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4 | protein | 46 | 0% helix, 13% strand | P40422 |
| N | Non template DNA 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP *GP*CP*TP)-3' | dna | 8 | — | — |
| P | Transcript RNA 5'-R(*CP*AP*GP*GP*AP)-3' | rna | 4 | — | — |
| T | Template DNA 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP *TP*TP*TP*CP*CP*BRU*GP*GP*TP*CP*AP*TP*TP)-3' | dna | 18 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A, B, P, T
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · chains A, P
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 | 1171 | 0.88 | 0.89 | 124 | empty |
| 2 | 1110 | 0.85 | 0.85 | 92 | empty |
| 3 | 646 | 0.82 | 0.86 | 75 | empty |
| 4 | 1143 | 0.81 | 0.82 | 122 | empty |
| 5 | 942 | 0.80 | 0.82 | 66 | empty |
Interfaces
35 interfaces between chains.
- A–B · 9607 Ų buried · 157 hydrogen bonds · protein-protein
- D–G · 2418 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 2220 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 2186 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 2069 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4A3E · RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with… · the same entry in another collection · chain I against I, 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 4A3E · PDBe 4A3E · 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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