MolNFT v1 · #145413 · protein + DNA
Yeast RNA polymerase III natural open complex (noc)
6CND · DNA-directed RNA polymerase III subunit RPC1: “Yeast RNA polymerase III natural open complex (noc)”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #145413 on GenesisL1: 3D structure, binding…
- PDB
- 6CND
- Type
- protein + DNA
- Length
- 5,869 residues
- Chains
- 21
- 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, P29056, P13393, P46678
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 21 distinct chains · 35% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase III subunit RPC1 (EC 2.7.7.6) | protein | 1428 | 39% helix, 10% strand | P04051 |
| B | DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6) | protein | 1114 | 26% helix, 20% strand | P22276 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 335 | 23% helix, 28% strand | P07703 |
| D | DNA-directed RNA polymerase III subunit RPC9 | protein | 119 | 51% helix, 4% strand | P47076 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 215 | 37% helix, 18% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 83 | 25% helix, 8% strand | P20435 |
| G | DNA-directed RNA polymerase III subunit RPC8 | protein | 184 | 9% helix, 26% strand | P35718 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 140 | 2% helix, 44% strand | P20436 |
| I | DNA-directed RNA polymerase III subunit RPC10 | protein | 42 | 0% helix, 17% strand | Q04307 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 67 | 49% helix, 3% strand | P22139 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 101 | 41% helix, 19% strand | P28000 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 46 | 0% helix, 17% strand | P40422 |
| M | DNA-directed RNA polymerase III subunit RPC5 | protein | 164 | 21% helix, 23% strand | P36121 |
| N | DNA-directed RNA polymerase III subunit RPC4 | protein | 110 | 18% helix, 18% strand | P25441 |
| O | DNA-directed RNA polymerase III subunit RPC3 | protein | 539 | 55% helix, 4% strand | P32349 |
| P | DNA-directed RNA polymerase III subunit RPC6 | protein | 277 | 43% helix, 8% strand | P32910 |
| Q | DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA- directed RNA polymerase III subunit RPC7 | protein | 54 | 41% helix, 2% strand | P17890 |
| R | Transcription factor iiib 70 kda SUBUNIT,TATA-box-binding PROTEIN,TRANSCRIPTION factor iiib 70 kda subunit | protein | 522 | 43% helix, 13% strand | P29056, P13393 |
| S | Transcription factor tfiiib component B'',TRANSCRIPTION factor tfiiib component B'',TRANSCRIPTION factor tfiiib component B'',TRANSCRIPTION factor tfiiib component B'',TRANSCRIPTION factor tfiiib component B'' | protein | 217 | 53% helix, 2% strand | P46678 |
| X | DNA (71-mer) | dna | 51 | — | — |
| Y | DNA (71-mer) | dna | 61 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, I, J, L, R
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 | 1062 | 0.86 | 0.86 | 130 | empty |
| 2 | 649 | 0.85 | 0.89 | 70 | empty |
| 3 | 871 | 0.83 | 0.85 | 98 | empty |
| 4 | 977 | 0.81 | 0.82 | 110 | empty |
| 5 | 754 | 0.79 | 0.83 | 81 | empty |
Interfaces
60 interfaces between chains.
- A–B · 8967 Ų buried · 105 hydrogen bonds · protein-protein
- A–O · 2846 Ų buried · 24 hydrogen bonds · protein-protein
- R–S · 2765 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 2460 Ų buried · 25 hydrogen bonds · protein-protein
- X–Y · 2329 Ų buried · 300 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- P04051 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC1… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P07703 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I and III subunit… · a predicted model of the same protein · chain C against A, TM-score 0.97
- P22276 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC2… · a predicted model of the same protein · chain B against A, TM-score 0.96
- P28000 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerases I and III subunit… · a predicted model of the same protein · chain K against A, TM-score 0.95
- P32349 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC3… · a predicted model of the same protein · chain O against A, TM-score 0.93
- P35718 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC8… · a predicted model of the same protein · chain G against A, TM-score 0.91
- P36121 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC5… · a predicted model of the same protein · chain M against A, TM-score 0.87
- P47076 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC9… · a predicted model of the same protein · chain D against A, TM-score 0.84
- P25441 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC4… · a predicted model of the same protein · chain N against A, TM-score 0.82
- P32910 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase III subunit RPC6… · a predicted model of the same protein · chain P against A, TM-score 0.71
- P46678 · AlphaFold monomer V2.0 prediction for transcription factor tfiiib component B'' (P46678) · a predicted model of the same protein · chain S against A, TM-score 0.64
- P29056 · AlphaFold monomer V2.0 prediction for transcription factor iiib 70 kda subunit (P29056) · a predicted model of the same protein · chain R against A, TM-score 0.64
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 P29056
- Every structure of UniProt P13393
- Every structure of UniProt P46678
- Elsewhere: RCSB PDB 6CND · PDBe 6CND · 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 P29056 · UniProt P13393 · UniProt P46678
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