MolNFT v1 · #114947 · protein + DNA + RNA
Crystal structure of a transcribing RNA polymerase II complex reveals a complete transcription bubble
5C4X · DNA-directed RNA polymerase II subunit RPB1: “Crystal structure of a transcribing RNA polymerase II complex reveals a complete transcription bubble”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT…
- PDB
- 5C4X
- Type
- protein + DNA + RNA
- Length
- 4,084 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
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 15 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1436 | 37% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1172 | 26% helix, 21% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 265 | 23% helix, 20% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 49% helix, 3% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 40% helix, 21% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 87 | 31% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 8% helix, 43% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 135 | 0% helix, 44% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 114 | 3% helix, 26% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 66 | 42% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 115 | 38% helix, 21% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 16% strand | P40422 |
| R | RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*A)-3') | rna | 9 | — | — |
| S | Non-template strand DNA (38-mer) | dna | 38 | — | — |
| U | Template strand DNA (40-mer) | dna | 40 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · 2 copies · chains A, R
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 | 935 | 0.88 | 0.90 | 119 | empty |
| 2 | 935 | 0.87 | 0.89 | 104 | empty |
| 3 | 871 | 0.84 | 0.86 | 94 | empty |
| 4 | 880 | 0.82 | 0.85 | 93 | empty |
| 5 | 662 | 0.82 | 0.87 | 75 | empty |
Interfaces
39 interfaces between chains.
- A–B · 9851 Ų buried · 142 hydrogen bonds · protein-protein
- D–G · 2549 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 2390 Ų buried · 32 hydrogen bonds · protein-protein
- A–F · 2338 Ų buried · 16 hydrogen bonds · protein-protein
- C–K · 2205 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5C4X · Crystal structure of a transcribing RNA Polymerase II complex reveals a complete… · the same entry in another collection · chain S against S, 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 5C4X · PDBe 5C4X · 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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