Research workbench
RNA polymerase III initially transcribing complex
Analyse RNA polymerase III initially transcribing complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F41
- Type
- protein + DNA + RNA
- Length
- 5,799 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase III subunit RPC1; DNA-directed RNA polymerase III subunit…
- EC
- 2.7.7.6
- UniProt
- P04051, P22276, P07703, P47076, P20434, P20435, P35718, P20436, Q04307, P22139, P28000, P40422, P36121, P25441, P32349, P32910, P17890, P13393, P29056, P46678
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 23 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase III subunit RPC1 (EC 2.7.7.6) | protein | 1398 | 35% helix, 12% strand | P04051 |
| B | DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6) | protein | 1114 | 23% helix, 20% strand | P22276 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 335 | 17% helix, 26% strand | P07703 |
| D | DNA-directed RNA polymerase III subunit RPC9 | protein | 119 | 51% helix, 3% strand | P47076 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 31% helix, 16% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 83 | 24% helix, 18% strand | P20435 |
| G | DNA-directed RNA polymerase III subunit RPC8 | protein | 180 | 11% helix, 30% strand | P35718 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 140 | 0% helix, 48% strand | P20436 |
| I | DNA-directed RNA polymerase III subunit RPC10 | protein | 34 | 9% helix, 21% strand | Q04307 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 67 | 43% helix, 3% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 101 | 43% helix, 22% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 20% strand | P40422 |
| M | DNA-directed RNA polymerase III subunit RPC5 | protein | 183 | 22% helix, 30% strand | P36121 |
| N | DNA-directed RNA polymerase III subunit RPC4 | protein | 104 | 22% helix, 35% strand | P25441 |
| O | DNA-directed RNA polymerase III subunit RPC3 | protein | 534 | 53% helix, 6% strand | P32349 |
| P | DNA-directed RNA polymerase III subunit RPC6 | protein | 246 | 43% helix, 8% strand | P32910 |
| Q | DNA-directed RNA polymerase III subunit RPC7 | protein | 35 | 31% helix, 3% strand | P17890 |
| U | Tata-box-binding protein | protein | 180 | 21% helix, 24% strand | P13393 |
| V | Transcription factor iiib 70 kda subunit | protein | 337 | 48% helix, 2% strand | P29056 |
| W | Transcription factor tfiiib component B'' | protein | 218 | 53% helix, 4% strand | P46678 |
| R | RNA | rna | 6 | — | — |
| X | Non-template DNA | dna | 60 | — | — |
| Y | Template-DNA | dna | 66 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, I, J, L, V
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 | 1020 | 0.88 | 0.89 | 135 | empty |
| 2 | 912 | 0.86 | 0.88 | 93 | empty |
| 3 | 1178 | 0.83 | 0.85 | 113 | empty |
| 4 | 563 | 0.83 | 0.88 | 65 | empty |
| 5 | 1111 | 0.83 | 0.84 | 91 | empty |
Interfaces
67 interfaces between chains.
- A–B · 8573 Ų buried · 80 hydrogen bonds · protein-protein
- A–O · 3015 Ų buried · 24 hydrogen bonds · protein-protein
- X–Y · 2662 Ų buried · 267 hydrogen bonds · nucleic-nucleic
- U–V · 2620 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 2331 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6F41 · RNA Polymerase III initially transcribing complex · the same entry in another collection · chain K against K, 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 P04051
- Every structure of UniProt P22276
- Every structure of UniProt P07703
- Every structure of UniProt P47076
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P35718
- Every structure of UniProt P20436
- Every structure of UniProt Q04307
- Every structure of UniProt P22139
- Every structure of UniProt P28000
- Every structure of UniProt P40422
- Every structure of UniProt P36121
- Every structure of UniProt P25441
- Every structure of UniProt P32349
- Every structure of UniProt P32910
- Every structure of UniProt P17890
- Every structure of UniProt P13393
- Every structure of UniProt P29056
- Every structure of UniProt P46678
- Elsewhere: RCSB PDB 6F41 · PDBe 6F41 · UniProt P04051 · UniProt P22276 · UniProt P07703 · UniProt P47076 · UniProt P20434 · UniProt P20435 · UniProt P35718 · UniProt P20436 · UniProt Q04307 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt P36121 · UniProt P25441 · UniProt P32349 · UniProt P32910 · UniProt P17890 · UniProt P13393 · UniProt P29056 · UniProt P46678
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