Research workbench
Structure of active transcription elongation complex pol II-dsif (SPT5-KOW5)-ELL2-EAF1 (composite structure)
Analyse Structure of active transcription elongation complex pol II-dsif… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OKX
- Type
- protein + DNA + RNA
- Length
- 4,236 residues
- Chains
- 18
- 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
- P11414, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A4X1VYD0, A0A4X1UK25, I3LN51, O00472, Q96JC9, O00267
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 18 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 | protein | 1407 | 41% helix, 16% strand | P11414 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1131 | 29% helix, 27% strand | I3LGP4 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 258 | 24% helix, 29% strand | I3LCH3 |
| D | RNA polymerase II subunit D | protein | 118 | 50% helix, 2% 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 | 11% helix, 48% strand | I3LJZ9 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 5% helix, 49% strand | A0A4X1ULF2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 116 | 4% helix, 31% 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 | 42% helix, 23% strand | A0A4X1UK25 |
| L | RNA polymerase II subunit K | protein | 44 | 0% helix, 30% strand | I3LN51 |
| M | RNA polymerase II elongation factor ELL2 | protein | 139 | 21% helix, 32% strand | O00472 |
| N | Non-template DNA | dna | 27 | — | — |
| O | Ell-associated factor 1 | protein | 106 | 3% helix, 48% strand | Q96JC9 |
| P | RNA | rna | 13 | — | — |
| T | Template DNA | dna | 39 | — | — |
| Z | Transcription elongation factor SPT5 | protein | 51 | 6% helix, 49% strand | O00267 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, Z, 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 | 1199 | 0.88 | 0.90 | 132 | empty |
| 2 | 1183 | 0.87 | 0.88 | 132 | empty |
| 3 | 827 | 0.86 | 0.89 | 85 | empty |
| 4 | 466 | 0.80 | 0.88 | 65 | empty |
| 5 | 766 | 0.79 | 0.83 | 59 | empty |
Interfaces
45 interfaces between chains.
- A–B · 9159 Ų buried · 147 hydrogen bonds · protein-protein
- M–O · 2537 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 2456 Ų buried · 37 hydrogen bonds · protein-protein
- C–K · 2325 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 2284 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7OKX · Structure of active transcription elongation complex Pol II-DSIF (SPT5-KOW5)-ELL2-EAF1… · the same entry in another collection · chain Z against Z, 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 P11414
- 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 O00472
- Every structure of UniProt Q96JC9
- Every structure of UniProt O00267
- Elsewhere: RCSB PDB 7OKX · PDBe 7OKX · UniProt P11414 · UniProt I3LGP4 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1VYD0 · UniProt A0A4X1UK25 · UniProt I3LN51 · UniProt O00472 · UniProt Q96JC9 · UniProt O00267
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