Research workbench
RNA polymerase II elongation complex with unnatural base DTPT3, rnam in swing state
Analyse RNA polymerase II elongation complex with unnatural base DTPT3, rnam in swing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KEF
- Type
- protein + DNA + RNA
- Length
- 3,590 residues
- Chains
- 13
- Method
- x-ray diffraction
- 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
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- WC4, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 13 distinct chains · 31% 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 | 1390 | 39% helix, 13% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1106 | 28% helix, 23% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 21% helix, 28% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 34% helix, 16% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 84 | 32% helix, 14% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 2% helix, 46% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 3% helix, 23% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 49% helix, 3% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 40% helix, 18% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 46 | 0% helix, 15% strand | P40422 |
| R | RNA | rna | 10 | — | — |
| T | Template strand DNA | dna | 28 | — | — |
| N | Non-template strand DNA | dna | 15 | — | — |
Ligands and binding sites
- WC4 · (1S)-1,4-anhydro-1-(3-methoxynaphthalen-2-yl)-5-O-phosphono-D-ribitol · ligand · chains A, B, R, T
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · chains A, R
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 | 1061 | 0.88 | 0.89 | 117 | empty |
| 2 | 1095 | 0.83 | 0.84 | 102 | empty |
| 3 | 611 | 0.80 | 0.85 | 72 | empty |
| 4 | 564 | 0.79 | 0.85 | 49 | empty |
| 5 | 510 | 0.78 | 0.85 | 54 | empty |
Interfaces
30 interfaces between chains.
- A–B · 9892 Ų buried · 134 hydrogen bonds · protein-protein
- A–E · 2222 Ų buried · 30 hydrogen bonds · protein-protein
- C–K · 2142 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1985 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1849 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 7KEF · RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state · 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 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
- Elsewhere: RCSB PDB 7KEF · PDBe 7KEF · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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