Research workbench
RNA polymerase II elongation complex at 5 mm MG2+ with GTP
Analyse RNA polymerase II elongation complex at 5 mm MG2+ with GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E2H
- Type
- protein + DNA + RNA
- Length
- 3,565 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
- GTP, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 13 distinct chains · 27% helix, 17% 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 | 1398 | 32% helix, 12% strand | P04050 |
| B | DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6) | protein | 1096 | 25% helix, 22% strand | P08518 |
| C | DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6) | protein | 266 | 25% helix, 22% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6) | protein | 193 | 30% helix, 16% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6) | protein | 83 | 25% helix, 12% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III 14.5 kda polypeptide (EC 2.7.7.6) | protein | 133 | 0% helix, 37% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6) | protein | 119 | 3% helix, 13% strand | P27999 |
| J | DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6) | protein | 65 | 49% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II 13.6 kda polypeptide (EC 2.7.7.6) | protein | 114 | 30% helix, 27% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III 7.7 kda polypeptide (EC 2.7.7.6) | protein | 46 | 0% helix, 13% strand | P40422 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains R, T, 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 | 940 | 0.87 | 0.89 | 105 | empty |
| 2 | 607 | 0.85 | 0.90 | 65 | empty |
| 3 | 779 | 0.80 | 0.84 | 71 | MG, GTP |
| 4 | 165 | 0.80 | 0.96 | 34 | empty |
| 5 | 1082 | 0.80 | 0.81 | 91 | empty |
Interfaces
31 interfaces between chains.
- A–B · 10189 Ų buried · 136 hydrogen bonds · protein-protein
- A–E · 2442 Ų buried · 23 hydrogen bonds · protein-protein
- C–K · 2128 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1874 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1852 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2E2H · RNA polymerase II elongation complex at 5 mM Mg2+ with GTP · the same entry in another collection · chain H against H, 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 2E2H · PDBe 2E2H · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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