Research workbench
8-oxoguanine containing RNA polymerase II elongation complex E
Analyse 8-oxoguanine containing RNA polymerase II elongation complex E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I4N
- Type
- protein + DNA + RNA
- Length
- 4,002 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
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 15 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1429 | 36% helix, 13% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1125 | 26% helix, 20% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 270 | 24% helix, 19% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 182 | 46% helix, 5% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 29% helix, 18% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 88 | 27% helix, 15% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 10% helix, 47% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 137 | 0% helix, 37% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 117 | 3% helix, 20% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 48% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 116 | 34% helix, 22% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 47 | 0% helix, 6% strand | P40422 |
| T | DNA (5'-D(*AP*G*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*AP*(8OG) P*GP*CP*CP*(BRU)P*GP*GP*TP*CP*AP*TP*T)-3') | dna | 20 | — | — |
| N | DNA (5'-D(*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3') | dna | 11 | — | — |
| P | RNA (5'-R(*UP*GP*CP*AP*UP*C*UP*UP*CP*CP*AP*GP*GP*CP*AP*U)- 3') | rna | 10 | — | — |
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 | 1100 | 0.89 | 0.90 | 126 | empty |
| 2 | 935 | 0.88 | 0.90 | 100 | empty |
| 3 | 1060 | 0.84 | 0.85 | 100 | empty |
| 4 | 615 | 0.81 | 0.86 | 63 | empty |
| 5 | 647 | 0.80 | 0.85 | 71 | empty |
Interfaces
38 interfaces between chains.
- A–B · 9696 Ų buried · 138 hydrogen bonds · protein-protein
- D–G · 2518 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 2182 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 2174 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 2068 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3I4N · 8-oxoguanine containing RNA polymerase II elongation complex E · the same entry in another collection · chain P against P, 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 3I4N · PDBe 3I4N · 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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