MolNFT v1 · #78214 · protein + DNA + RNA
RNA polymerase II initiation complex with a 5-nt RNA containing a 5BR- U
3S2D · DNA-directed RNA polymerase II subunit RPB1: “RNA polymerase II initiation complex with a 5-nt RNA containing a 5BR- U”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #78214 on GenesisL1: 3D…
- PDB
- 3S2D
- Type
- protein + DNA + RNA
- Length
- 3,579 residues
- Chains
- 12
- 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 0.88
Structure
x-ray diffraction · 12 distinct chains · 32% 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 | 1405 | 40% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1114 | 29% helix, 24% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 26% helix, 26% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 39% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 85 | 31% helix, 14% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 0% helix, 46% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 4% helix, 26% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 46% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 37% helix, 20% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 46 | 7% helix, 15% strand | P40422 |
| R | RNA (5'-R(*AP*GP*GP*(5BU)P*G)-3') | rna | 5 | — | — |
| T | DNA (5'- D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP* CP*TP*CP*GP*AP*TP*G)-3') | dna | 13 | — | — |
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 | 950 | 0.88 | 0.90 | 115 | empty |
| 2 | 844 | 0.86 | 0.89 | 85 | empty |
| 3 | 696 | 0.85 | 0.89 | 73 | empty |
| 4 | 1110 | 0.81 | 0.82 | 138 | empty |
| 5 | 549 | 0.80 | 0.86 | 50 | empty |
Interfaces
26 interfaces between chains.
- A–B · 9651 Ų buried · 146 hydrogen bonds · protein-protein
- A–E · 2353 Ų buried · 32 hydrogen bonds · protein-protein
- C–K · 2161 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1890 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1848 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3S2D · RNA Polymerase II Initiation Complex with a 5-nt RNA containing a 5Br-U · 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 3S2D · PDBe 3S2D · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422
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