MolNFT v1 · #110716 · protein + DNA + RNA
Crystal structure of 5-carboxycytosine recognition by RNA polymerase II during transcription elongation.
4Y52 · DNA-directed RNA polymerase II subunit RPB1: “Crystal structure of 5-carboxycytosine recognition by RNA polymerase II during transcription elongation.”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.89).…
- PDB
- 4Y52
- Type
- protein + DNA + RNA
- Length
- 3,588 residues
- Chains
- 13
- 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, P20434, P20435, P20436, P27999, P22139, P38902, P40422
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 13 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1393 | 38% helix, 14% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1103 | 29% helix, 25% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 24% helix, 23% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 37% helix, 21% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 84 | 31% helix, 14% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 2% helix, 44% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 4% helix, 25% 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 | 36% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 16% strand | P40422 |
| T | DNA (29-mer) | dna | 29 | — | — |
| N | DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3') | dna | 14 | — | — |
| R | RNA (5'-D(*AP*UP*GP*GP*AP*GP*AP*GP*G)-3') | rna | 9 | — | — |
Ligands and binding sites
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 | 1103 | 0.89 | 0.90 | 127 | empty |
| 2 | 595 | 0.84 | 0.90 | 55 | empty |
| 3 | 767 | 0.84 | 0.87 | 77 | empty |
| 4 | 588 | 0.79 | 0.85 | 58 | empty |
| 5 | 938 | 0.78 | 0.81 | 82 | empty |
Interfaces
30 interfaces between chains.
- A–B · 9797 Ų buried · 152 hydrogen bonds · protein-protein
- A–E · 2210 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 2136 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1826 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1787 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4Y52 · Crystal structure of 5-Carboxycytosine Recognition by RNA Polymerase II during… · 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 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 4Y52 · PDBe 4Y52 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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