Research workbench
Complete RNA polymerase II elongation complex with substrate analogue gmpcpp
Analyse Complete RNA polymerase II elongation complex with substrate analogue gmpcpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y77
- Type
- protein + DNA + RNA
- Length
- 3,953 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP *CP*TP*G)-3'…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
- Ligands
- G2P, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 15 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP *CP*TP*G)-3' | dna | 19 | — | — |
| N | 5'-D(*AP*AP*GP*TP*AP*CP*T)-3' | dna | 7 | — | — |
| P | 5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' | rna | 10 | — | — |
| A | DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6) | protein | 1416 | 38% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6) | protein | 1112 | 26% helix, 19% strand | P08518 |
| C | DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6) | protein | 266 | 23% helix, 16% strand | P16370 |
| D | DNA-directed RNA polymerase II 32 kda polypeptide (EC 2.7.7.6) | protein | 177 | 46% helix, 6% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6) | protein | 214 | 35% helix, 20% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6) | protein | 84 | 27% helix, 15% strand | P20435 |
| G | DNA-directed RNA polymerase II 19 kda polypeptide (EC 2.7.7.6) | protein | 171 | 9% helix, 47% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III 14.5 kda polypeptide (EC 2.7.7.6) | protein | 133 | 5% helix, 43% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6) | protein | 119 | 0% helix, 19% 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 | 37% helix, 22% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III 7.7 kda polypeptide (EC 2.7.7.6) | protein | 46 | 0% helix, 9% strand | P40422 |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains T, P, A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · chains P, A
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 | 833 | 0.89 | 0.92 | 105 | empty |
| 2 | 629 | 0.87 | 0.92 | 76 | empty |
| 3 | 972 | 0.83 | 0.84 | 87 | empty |
| 4 | 940 | 0.82 | 0.83 | 98 | empty |
| 5 | 573 | 0.79 | 0.85 | 50 | empty |
Interfaces
37 interfaces between chains.
- A–B · 9822 Ų buried · 131 hydrogen bonds · protein-protein
- D–G · 2297 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 2220 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 2163 Ų buried · 16 hydrogen bonds · protein-protein
- C–K · 2149 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1Y77 · Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP · the same entry in another collection · chain L against L, 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 P20433
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- 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 1Y77 · PDBe 1Y77 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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