Research workbench
RNA polymerase II initial transcribing complex with a 7NT DNA-RNA hybrid and soaked with ampcpp
Analyse RNA polymerase II initial transcribing complex with a 7NT 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
- 4A3L
- Type
- protein + DNA + RNA
- Length
- 3,964 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 0.89
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 | 1425 | 41% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1115 | 28% helix, 23% 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 | 51% helix, 6% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 36% helix, 22% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 84 | 33% helix, 15% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 13% helix, 50% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 0% helix, 41% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 0% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 45% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 38% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 46 | 0% helix, 9% strand | P40422 |
| N | 5'-D(*AP*AP*GP*TP*AP*CP*TP)-3' | dna | 9 | — | — |
| P | 5'-R(*AP*CP*CP*AP*GP*GP*AP)-3' | rna | 7 | — | — |
| T | 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*T)-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 | 1003 | 0.89 | 0.91 | 121 | empty |
| 2 | 1029 | 0.87 | 0.89 | 104 | APC |
| 3 | 1076 | 0.85 | 0.86 | 87 | empty |
| 4 | 883 | 0.80 | 0.82 | 92 | empty |
| 5 | 702 | 0.79 | 0.84 | 67 | empty |
Interfaces
36 interfaces between chains.
- A–B · 9682 Ų buried · 156 hydrogen bonds · protein-protein
- D–G · 2487 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 2267 Ų buried · 31 hydrogen bonds · protein-protein
- C–K · 2227 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 2087 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4A3L · RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with… · the same entry in another collection · chain J against J, 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 4A3L · PDBe 4A3L · 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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