MolNFT v1 · #46153 · protein + DNA + RNA
RNA polymerase II elongation complex in 5 mm MG+2 with 2'- dutp
2NVX · 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3': “RNA polymerase II elongation complex in 5 mm MG+2 with 2'- dutp”. X-ray diffraction, 3 ligands (DUT, ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #46153 on GenesisL1: 3D structure…
- PDB
- 2NVX
- Type
- protein + DNA + RNA
- Length
- 3,614 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'; 5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- DUT, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 13 distinct chains · 28% 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 | — | — |
| N | 5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)- 3' | dna | 14 | — | — |
| T | 28-mer DNA template strand | dna | 28 | — | — |
| A | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 1402 | 35% helix, 13% strand | P04050 |
| B | DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6) | protein | 1114 | 26% helix, 21% strand | P08518 |
| C | DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6) | protein | 266 | 23% helix, 25% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6) | protein | 214 | 30% helix, 21% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6) | protein | 88 | 30% helix, 14% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III 14.5 kda polypeptide (EC 2.7.7.6) | protein | 134 | 2% helix, 44% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6) | protein | 119 | 3% helix, 22% strand | P27999 |
| J | DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6) | protein | 65 | 34% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II 13.6 kda polypeptide (EC 2.7.7.6) | protein | 114 | 39% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III 7.7 kda polypeptide (EC 2.7.7.6) | protein | 46 | 0% helix, 17% strand | P40422 |
Ligands and binding sites
- DUT · Deoxyuridine-5'-triphosphate · ligand · chains R, A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · chains 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 | 991 | 0.88 | 0.90 | 125 | empty |
| 2 | 665 | 0.85 | 0.90 | 66 | empty |
| 3 | 979 | 0.82 | 0.83 | 71 | empty |
| 4 | 678 | 0.80 | 0.85 | 65 | empty |
| 5 | 174 | 0.80 | 0.95 | 32 | empty |
Interfaces
32 interfaces between chains.
- A–B · 10075 Ų buried · 120 hydrogen bonds · protein-protein
- A–E · 2371 Ų buried · 31 hydrogen bonds · protein-protein
- C–K · 2143 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1895 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1876 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2NVX · RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP · the same entry in another collection · chain R against R, 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 2NVX · PDBe 2NVX · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.