Research workbench
Structure of active transcription elongation complex pol II-dsif (SPT5-KOW5)
Analyse Structure of active transcription elongation complex pol II-dsif (SPT5-KOW5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OL0
- Type
- protein + DNA + RNA
- Length
- 3,991 residues
- Chains
- 16
- 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
- I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A4X1VYD0, A0A4X1UK25, I3LN51, O00267
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 16 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 | protein | 1407 | 41% helix, 15% strand | — |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1131 | 28% helix, 27% strand | I3LGP4 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 258 | 23% helix, 29% strand | I3LCH3 |
| D | RNA polymerase II subunit D | protein | 118 | 53% helix, 3% strand | A0A287ADR4 |
| E | DNA-directed RNA polymerase II subunit E | protein | 209 | 36% helix, 24% strand | I3LSI7 |
| F | DNA-directed RNA polymerase II subunit F | protein | 78 | 37% helix, 18% strand | F1SKN8 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 12% helix, 41% strand | I3LJZ9 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 3% helix, 49% strand | A0A4X1ULF2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 116 | 9% helix, 29% strand | P60899 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 66 | 42% helix, 5% strand | A0A4X1VYD0 |
| K | RNA_POL_L_2 domain-containing protein | protein | 115 | 43% helix, 23% strand | A0A4X1UK25 |
| L | RNA polymerase II subunit K | protein | 44 | 0% helix, 30% strand | I3LN51 |
| Z | Transcription elongation factor SPT5 | protein | 51 | 6% helix, 49% strand | O00267 |
| P | RNA | rna | 13 | — | — |
| N | Non-template DNA | dna | 27 | — | — |
| T | Template DNA | dna | 39 | — | — |
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 | 810 | 0.88 | 0.91 | 101 | empty |
| 2 | 1110 | 0.87 | 0.88 | 118 | empty |
| 3 | 796 | 0.85 | 0.88 | 94 | empty |
| 4 | 515 | 0.80 | 0.87 | 64 | empty |
| 5 | 1143 | 0.80 | 0.82 | 86 | empty |
Interfaces
41 interfaces between chains.
- A–B · 9199 Ų buried · 155 hydrogen bonds · protein-protein
- A–E · 2434 Ų buried · 33 hydrogen bonds · protein-protein
- C–K · 2362 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 2209 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 2149 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7OL0 · Structure of active transcription elongation complex Pol II-DSIF (SPT5-KOW5) · the same entry in another collection · chain T against T, 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 I3LGP4
- Every structure of UniProt I3LCH3
- Every structure of UniProt A0A287ADR4
- Every structure of UniProt I3LSI7
- Every structure of UniProt F1SKN8
- Every structure of UniProt I3LJZ9
- Every structure of UniProt A0A4X1ULF2
- Every structure of UniProt P60899
- Every structure of UniProt A0A4X1VYD0
- Every structure of UniProt A0A4X1UK25
- Every structure of UniProt I3LN51
- Every structure of UniProt O00267
- Elsewhere: RCSB PDB 7OL0 · PDBe 7OL0 · UniProt I3LGP4 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1VYD0 · UniProt A0A4X1UK25 · UniProt I3LN51 · UniProt O00267
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