Research workbench
Crystal structure of RNA polymerase II in complex with tfiib
Analyse Crystal structure of RNA polymerase II in complex with tfiib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K1F
- Type
- protein
- Length
- 4,115 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, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, B3LK56
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 13 distinct chains · 32% 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 | 1416 | 40% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1120 | 28% helix, 22% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 (EC 2.7.7.6) | protein | 266 | 24% helix, 25% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 (EC 2.7.7.6) | protein | 178 | 48% helix, 6% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 (EC 2.7.7.6) | protein | 214 | 38% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 (EC 2.7.7.6) | protein | 87 | 30% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 (EC 2.7.7.6) | protein | 171 | 10% helix, 47% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 (EC 2.7.7.6) | protein | 134 | 0% helix, 42% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 (EC 2.7.7.6) | protein | 119 | 3% helix, 24% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 (EC 2.7.7.6) | protein | 65 | 45% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 (EC 2.7.7.6) | protein | 114 | 38% helix, 20% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 (EC 2.7.7.6) | protein | 46 | 0% helix, 15% strand | P40422 |
| M | Transcription initiation factor iib | protein | 185 | 50% helix, 7% strand | B3LK56 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, I, J, L, M
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 | 1176 | 0.87 | 0.88 | 154 | empty |
| 2 | 1102 | 0.85 | 0.86 | 84 | empty |
| 3 | 754 | 0.82 | 0.85 | 60 | empty |
| 4 | 1157 | 0.80 | 0.82 | 94 | empty |
| 5 | 968 | 0.79 | 0.81 | 142 | empty |
Interfaces
30 interfaces between chains.
- A–B · 10309 Ų buried · 154 hydrogen bonds · protein-protein
- D–G · 2532 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 2280 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2255 Ų buried · 20 hydrogen bonds · protein-protein
- C–K · 2136 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3K1F · Crystal structure of RNA Polymerase II in complex with TFIIB · the same entry in another collection · chain M against M, 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 B3LK56
- Elsewhere: RCSB PDB 3K1F · PDBe 3K1F · 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 B3LK56
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