Research workbench
Structure of an RNA polymerase II-dsif transcription elongation complex
Analyse Structure of an RNA polymerase II-dsif transcription elongation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OIK
- Type
- protein + DNA + RNA
- Length
- 4,610 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- A5PJW8, Q3T0Q3, Q1JQ91, Q2T9T3, F2Z4C9, Q5E9B8, F2Z4H3, Q32P73, Q32P78, Q32P79, Q3ZBC0, P63272, O00267
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 17 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1421 | 41% helix, 15% strand | — |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1147 | 27% helix, 25% strand | A5PJW8 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 259 | 23% helix, 28% strand | Q3T0Q3 |
| D | Polymerase (RNA) II (DNA directed) polypeptide D | protein | 128 | 60% helix, 4% strand | Q1JQ91 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 209 | 36% helix, 20% strand | Q2T9T3 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 82 | 28% helix, 16% strand | F2Z4C9 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 55% strand | Q5E9B8 |
| H | Uncharacterized protein | protein | 148 | 0% helix, 51% strand | F2Z4H3 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 117 | 7% helix, 26% strand | Q32P73 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 67 | 40% helix, 1% strand | Q32P78 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 115 | 38% helix, 23% strand | Q32P79 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 27% strand | Q3ZBC0 |
| N | DNA (43-mer) | dna | 34 | — | — |
| P | RNA (5'- R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3') | rna | 20 | — | — |
| T | DNA (43-mer) | dna | 43 | — | — |
| Y | Transcription elongation factor SPT4 | protein | 116 | 33% helix, 22% strand | P63272 |
| Z | Transcription elongation factor SPT5 | protein | 488 | 13% helix, 36% strand | O00267 |
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 | 716 | 0.87 | 0.91 | 93 | empty |
| 2 | 1102 | 0.85 | 0.87 | 106 | empty |
| 3 | 600 | 0.84 | 0.89 | 68 | empty |
| 4 | 742 | 0.83 | 0.86 | 83 | empty |
| 5 | 541 | 0.83 | 0.89 | 62 | empty |
Interfaces
47 interfaces between chains.
- A–B · 9327 Ų buried · 124 hydrogen bonds · protein-protein
- A–E · 2412 Ų buried · 22 hydrogen bonds · protein-protein
- C–K · 2267 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 2262 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 2224 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5OIK · Structure of an RNA polymerase II-DSIF transcription elongation complex · the same entry in another collection · chain K against K, 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 A5PJW8
- Every structure of UniProt Q3T0Q3
- Every structure of UniProt Q1JQ91
- Every structure of UniProt Q2T9T3
- Every structure of UniProt F2Z4C9
- Every structure of UniProt Q5E9B8
- Every structure of UniProt F2Z4H3
- Every structure of UniProt Q32P73
- Every structure of UniProt Q32P78
- Every structure of UniProt Q32P79
- Every structure of UniProt Q3ZBC0
- Every structure of UniProt P63272
- Every structure of UniProt O00267
- Elsewhere: RCSB PDB 5OIK · PDBe 5OIK · UniProt A5PJW8 · UniProt Q3T0Q3 · UniProt Q1JQ91 · UniProt Q2T9T3 · UniProt F2Z4C9 · UniProt Q5E9B8 · UniProt F2Z4H3 · UniProt Q32P73 · UniProt Q32P78 · UniProt Q32P79 · UniProt Q3ZBC0 · UniProt P63272 · UniProt O00267
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.