MolNFT v1 · #179733 · protein + DNA + RNA
RNA polymerase II elongation complex with unnatural base DTPT3, rnam in swing state
7KEF · DNA-directed RNA polymerase II subunit RPB1: “RNA polymerase II elongation complex with unnatural base DTPT3, rnam in swing state”. X-ray diffraction, 3 ligands (WC4, ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #179733…
- 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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