Research workbench
RNA polymerase II elongation complex in 150 mm MG+2 with UTP
Analyse RNA polymerase II elongation complex in 150 mm MG+2 with UTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YU9
- Type
- protein + DNA + RNA
- Length
- 3,626 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'; 28-mer DNA template strand…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- UTP, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 13 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' | rna | 10 | — | — |
| T | 28-mer DNA template strand | dna | 28 | — | — |
| N | 5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3' | dna | 14 | — | — |
| A | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 1411 | 32% helix, 14% strand | P04050 |
| B | DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6) | protein | 1121 | 25% helix, 22% strand | P08518 |
| C | DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6) | protein | 266 | 22% helix, 21% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6) | protein | 214 | 36% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6) | protein | 85 | 31% helix, 14% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III 14.5 kda polypeptide (EC 2.7.7.6) | protein | 133 | 2% helix, 46% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6) | protein | 119 | 0% helix, 26% strand | P27999 |
| J | DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6) | protein | 65 | 46% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II 13.6 kda polypeptide (EC 2.7.7.6) | protein | 114 | 39% helix, 23% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III 7.7 kda polypeptide (EC 2.7.7.6) | protein | 46 | 0% helix, 15% strand | P40422 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · 2 copies · chains R, A, B
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 | 945 | 0.88 | 0.90 | 119 | empty |
| 2 | 1064 | 0.88 | 0.89 | 114 | empty |
| 3 | 1150 | 0.84 | 0.85 | 94 | empty |
| 4 | 1129 | 0.81 | 0.83 | 102 | empty |
| 5 | 614 | 0.79 | 0.85 | 61 | empty |
Interfaces
31 interfaces between chains.
- A–B · 9782 Ų buried · 112 hydrogen bonds · protein-protein
- A–E · 2326 Ų buried · 25 hydrogen bonds · protein-protein
- C–K · 2165 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 2029 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1890 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2YU9 · RNA polymerase II elongation complex in 150 mm MG+2 with UTP · 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 2YU9 · PDBe 2YU9 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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