Research workbench
Structure of transcribing RNA polymerase II-nucleosome complex
Analyse Structure of transcribing RNA polymerase II-nucleosome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I84
- Type
- protein + DNA + RNA
- Length
- 5,002 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H2A type 1; DNA (170-mer); DNA (158-mer); Histone H4; Histone H2B…
- EC
- 2.7.7.6
- UniProt
- P84233, P06897, P62799, P02281, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 23 distinct chains · 35% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Histone H3.2 | protein | 97 | 65% helix, 3% strand | P84233 |
| Q | Histone H2A type 1 | protein | 103 | 49% helix, 3% strand | P06897 |
| V | Histone H2A type 1 | protein | 105 | 46% helix, 5% strand | P06897 |
| T | DNA (170-mer) | dna | 169 | — | — |
| N | DNA (158-mer) | dna | 158 | — | — |
| O | Histone H4 | protein | 83 | 54% helix, 5% strand | P62799 |
| R | Histone H2B 1.1 | protein | 95 | 63% helix, 1% strand | P02281 |
| S | Histone H3.2 | protein | 97 | 66% helix, 1% strand | P84233 |
| U | Histone H4 | protein | 78 | 50% helix, 4% strand | P62799 |
| W | Histone H2B 1.1 | protein | 93 | 75% helix, 4% strand | P02281 |
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1416 | 39% helix, 11% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1104 | 28% helix, 17% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 24% helix, 21% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 48% helix, 4% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 36% helix, 18% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 87 | 28% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 9% helix, 40% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 134 | 0% helix, 35% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 4% helix, 21% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 51% helix, 0% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 39% helix, 25% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 46 | 0% helix, 15% strand | P40422 |
| P | RNA | 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 | 836 | 0.85 | 0.88 | 104 | empty |
| 2 | 737 | 0.85 | 0.89 | 75 | empty |
| 3 | 894 | 0.84 | 0.86 | 80 | empty |
| 4 | 726 | 0.83 | 0.86 | 68 | empty |
| 5 | 1002 | 0.81 | 0.82 | 82 | empty |
Interfaces
73 interfaces between chains.
- A–B · 9763 Ų buried · 119 hydrogen bonds · protein-protein
- T–N · 7720 Ų buried · 762 hydrogen bonds · nucleic-nucleic
- M–O · 2609 Ų buried · 23 hydrogen bonds · protein-protein
- Q–R · 2595 Ų buried · 18 hydrogen bonds · protein-protein
- V–W · 2494 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6I84 · Structure of transcribing RNA polymerase II-nucleosome complex · the same entry in another collection · chain A against A, 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 P84233
- Every structure of UniProt P06897
- Every structure of UniProt P62799
- Every structure of UniProt P02281
- 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 6I84 · PDBe 6I84 · UniProt P84233 · UniProt P06897 · UniProt P62799 · UniProt P02281 · 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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