MolNFT v1 · #119012 · protein
Cryo-EM structure of yeast RNA polymerase III at 4.7 a
5FJA · DNA-directed RNA polymerase III subunit RPC1: “Cryo-EM structure of yeast RNA polymerase III at 4.7 a”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #119012 on GenesisL1: 3D structure, binding…
- PDB
- 5FJA
- Type
- protein
- Length
- 4,845 residues
- Chains
- 17
- 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
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 17 distinct chains · 31% 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 | 1403 | 36% helix, 10% strand | P04051 |
| B | DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6) | protein | 1114 | 26% helix, 21% strand | P22276 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 335 | 20% helix, 27% strand | P07703 |
| D | DNA-directed RNA polymerase III subunit RPC9 | protein | 119 | 46% helix, 3% strand | P47076 |
| E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1 | protein | 215 | 31% helix, 16% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2 | protein | 83 | 31% helix, 7% strand | P20435 |
| G | DNA-directed RNA polymerase III subunit RPC8 | protein | 182 | 9% helix, 37% strand | P35718 |
| H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3 | protein | 140 | 0% helix, 47% strand | P20436 |
| I | DNA-directed RNA polymerase III subunit RPC10 | protein | 92 | 0% helix, 35% strand | Q04307 |
| J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5 | protein | 67 | 42% helix, 3% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 101 | 41% helix, 18% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4 | protein | 45 | 0% helix, 22% strand | P40422 |
| M | DNA-directed RNA polymerase III subunit RPC5 | protein | 164 | 20% helix, 23% strand | P36121 |
| N | DNA-directed RNA polymerase III subunit RPC4 | protein | 110 | 22% helix, 19% strand | P25441 |
| O | DNA-directed RNA polymerase III subunit RPC3 | protein | 539 | 53% helix, 5% strand | P32349 |
| P | DNA-directed RNA polymerase III subunit RPC6 | protein | 89 | 27% helix, 8% strand | P32910 |
| Q | DNA-directed RNA polymerase III subunit RPC7 | protein | 47 | 53% helix, 0% strand | P17890 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, I, J, L
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 | 1080 | 0.86 | 0.87 | 130 | empty |
| 2 | 885 | 0.86 | 0.88 | 111 | empty |
| 3 | 1131 | 0.84 | 0.85 | 114 | empty |
| 4 | 950 | 0.84 | 0.85 | 104 | empty |
| 5 | 842 | 0.81 | 0.84 | 88 | empty |
Interfaces
38 interfaces between chains.
- A–B · 8824 Ų buried · 78 hydrogen bonds · protein-protein
- A–O · 2783 Ų buried · 11 hydrogen bonds · protein-protein
- C–K · 2346 Ų buried · 7 hydrogen bonds · protein-protein
- M–N · 2303 Ų buried · 43 hydrogen bonds · protein-protein
- A–E · 2265 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FJA · Cryo-EM structure of yeast RNA polymerase III at 4.7 A · the same entry in another collection · chain J against J, 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
- Elsewhere: RCSB PDB 5FJA · PDBe 5FJA · 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
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