MolNFT v1 · #87348 · protein + DNA + RNA
Elongating RNA polymerase II-BYE1 tld complex
4BY7 · DNA-directed RNA polymerase II subunit RPB1: “Elongating RNA polymerase II-BYE1 tld complex”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #87348 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4BY7
- Type
- protein + DNA + RNA
- Length
- 4,102 residues
- Chains
- 16
- 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, P36106
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 16 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1426 | 40% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1115 | 28% helix, 24% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 25% helix, 28% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 51% helix, 5% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1 | protein | 215 | 42% helix, 22% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2 | protein | 87 | 33% helix, 15% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 13% helix, 48% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3 | protein | 133 | 2% helix, 46% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 4% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5 | protein | 65 | 43% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 37% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4 | protein | 46 | 0% helix, 13% strand | P40422 |
| N | , 5'-D(*DAP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*DTP)-3' | dna | 13 | — | — |
| P | 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' | rna | 10 | — | — |
| T | 5'-D(*DAP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*DAP *TP*TP*CP*CP*BP*GP*GP*TP*CP*AP*TP*T)-3' | dna | 25 | — | — |
| X | Transcription factor BYE1 | protein | 119 | 67% helix, 0% strand | P36106 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · chains A, P
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, D, G
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 | 112 | empty |
| 2 | 1141 | 0.88 | 0.90 | 117 | empty |
| 3 | 1067 | 0.84 | 0.85 | 87 | empty |
| 4 | 1042 | 0.82 | 0.83 | 100 | empty |
| 5 | 881 | 0.80 | 0.82 | 93 | empty |
Interfaces
38 interfaces between chains.
- A–B · 9888 Ų buried · 151 hydrogen bonds · protein-protein
- D–G · 2338 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 2231 Ų buried · 28 hydrogen bonds · protein-protein
- C–K · 2143 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 2126 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4BY7 · elongating RNA Polymerase II-Bye1 TLD complex · the same entry in another collection · chain X against X, 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
- Every structure of UniProt P36106
- Elsewhere: RCSB PDB 4BY7 · PDBe 4BY7 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P36106
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