Research workbench
RNA polymerase II-SPT4/5-nucleosome-CHD1 structure
Analyse RNA polymerase II-SPT4/5-nucleosome-CHD1 structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NKX
- Type
- protein + DNA + RNA
- Length
- 5,788 residues
- Chains
- 26
- Method
- electron microscopy
- 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, 3.6.4.-
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422, P84233, P62799, P06897, P02281, P32657, A0A6A5PX04, P27692, P20433, P34087
- Ligands
- ADP, BEF, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 26 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1409 | 42% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1116 | 28% helix, 22% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 265 | 24% helix, 28% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 39% helix, 21% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 87 | 31% helix, 14% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 4% helix, 51% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 3% helix, 27% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 52% helix, 5% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 39% helix, 22% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 16% strand | P40422 |
| a | Histone H3.2 | protein | 76 | 71% helix, 1% strand | P84233 |
| b | Histone H4 | protein | 80 | 66% helix, 5% strand | P62799 |
| c | Histone H2A type 1 | protein | 103 | 53% helix, 6% strand | P06897 |
| d | Histone H2B 1.1 | protein | 92 | 71% helix, 3% strand | P02281 |
| e | Histone H3.2 | protein | 97 | 66% helix, 1% strand | P84233 |
| f | Histone H4 | protein | 78 | 65% helix, 5% strand | P62799 |
| g | Histone H2A type 1 | protein | 93 | 62% helix, 6% strand | P06897 |
| h | Histone H2B 1.1 | protein | 93 | 72% helix, 3% strand | P02281 |
| T | DNA (139-mer) | dna | 139 | — | — |
| N | DNA (128-mer) | dna | 128 | — | — |
| W | Chromo domain-containing protein 1 (EC 3.6.4.-) | protein | 622 | 44% helix, 16% strand | P32657 |
| P | RNA | rna | 16 | — | — |
| Y | Chromatin elongation factor SPT4 | protein | 98 | 30% helix, 21% strand | A0A6A5PX04 |
| Z | Transcription elongation factor SPT5 | protein | 156 | 21% helix, 31% strand | P27692 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 180 | 53% helix, 4% strand | P20433 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 49% strand | P34087 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains W
- BEF · Beryllium trifluoride ion · ligand · chains W
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, 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 | 1177 | 0.89 | 0.90 | 136 | empty |
| 2 | 815 | 0.86 | 0.89 | 85 | empty |
| 3 | 993 | 0.84 | 0.85 | 98 | empty |
| 4 | 1187 | 0.84 | 0.85 | 127 | empty |
| 5 | 756 | 0.84 | 0.87 | 91 | empty |
Interfaces
82 interfaces between chains.
- A–B · 9614 Ų buried · 142 hydrogen bonds · protein-protein
- T–N · 5745 Ų buried · 436 hydrogen bonds · nucleic-nucleic
- c–d · 2608 Ų buried · 19 hydrogen bonds · protein-protein
- g–h · 2598 Ų buried · 26 hydrogen bonds · protein-protein
- e–f · 2473 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7NKX · RNA polymerase II-Spt4/5-nucleosome-Chd1 structure · the same entry in another collection · chain J against J, 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 P20434
- Every structure of UniProt P20435
- 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
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt P32657
- Every structure of UniProt A0A6A5PX04
- Every structure of UniProt P27692
- Every structure of UniProt P20433
- Every structure of UniProt P34087
- Elsewhere: RCSB PDB 7NKX · PDBe 7NKX · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt P32657 · UniProt A0A6A5PX04 · UniProt P27692 · UniProt P20433 · UniProt P34087
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