MolNFT v1 · #129731 · protein + DNA + RNA
RNA polymerase II elongation complex in the presence of 3D-napht-a
5OT2 · DNA-directed RNA polymerase II subunit RPB1: “RNA polymerase II elongation complex in the presence of 3D-napht-a”. X-ray diffraction, 3 ligands (AHW, ZN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #129731 on GenesisL1: 3D…
- PDB
- 5OT2
- Type
- protein + DNA + RNA
- Length
- 3,933 residues
- Chains
- 15
- 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, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
- Ligands
- AHW, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 15 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1412 | 42% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1104 | 29% helix, 23% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 265 | 25% helix, 30% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 175 | 53% helix, 7% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 212 | 41% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 87 | 33% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 13% helix, 50% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 134 | 0% helix, 50% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 114 | 0% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 43% helix, 5% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 39% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 27% strand | P40422 |
| T | DNA template strand | dna | 19 | — | — |
| N | DNA non-template strand | dna | 7 | — | — |
| P | RNA product strand | rna | 10 | — | — |
Ligands and binding sites
- AHW · 2-ethyl-7-methoxy-naphthalene · ligand · chains A, T
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · chains A, P
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 | 917 | 0.89 | 0.91 | 112 | empty |
| 2 | 1062 | 0.86 | 0.88 | 94 | empty |
| 3 | 632 | 0.82 | 0.87 | 91 | empty |
| 4 | 1129 | 0.82 | 0.83 | 106 | empty |
| 5 | 522 | 0.81 | 0.87 | 56 | empty |
Interfaces
37 interfaces between chains.
- A–B · 9587 Ų buried · 143 hydrogen bonds · protein-protein
- D–G · 2443 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2183 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 2150 Ų buried · 20 hydrogen bonds · protein-protein
- C–K · 2077 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified, 1 covalent (disulfide, nucleotide modification, covalent ligand).
Compared structures
- 5OT2 · RNA polymerase II elongation complex in the presence of 3d-Napht-A · 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 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 5OT2 · PDBe 5OT2 · 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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