MolNFT v1 · #178543 · protein + DNA + RNA
Human pol III pre-termination complex
7FJJ · DNA-directed RNA polymerase III subunit RPC1: “Human pol III pre-termination complex”. Electron microscopy, 3 ligands (SF4, ZN, MG), 20 pockets (best druggability 0.82). MolNFT v1 #178543 on GenesisL1: 3D structure, binding sites…
- PDB
- 7FJJ
- Type
- protein + DNA + RNA
- Length
- 4,895 residues
- Chains
- 20
- 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
- O14802, Q9NW08, O15160, O75575, P19388, P61218, Q9Y535, P52434, Q9Y2Y1, P62875, P0DPB6, P53803, Q9NVU0, P05423, Q9BUI4, Q9H1D9, O15318
- Ligands
- SF4, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 20 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase III subunit RPC1 (EC 2.7.7.6) | protein | 1360 | 39% helix, 14% strand | O14802 |
| B | DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6) | protein | 1095 | 30% helix, 25% strand | Q9NW08 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 343 | 29% helix, 31% strand | O15160 |
| D | DNA-directed RNA polymerase III subunit RPC9 | protein | 122 | 61% helix, 2% strand | O75575 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 209 | 41% helix, 23% strand | P19388 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 76 | 34% helix, 17% strand | P61218 |
| G | DNA-directed RNA polymerase III subunit RPC8 | protein | 166 | 8% helix, 36% strand | Q9Y535 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 2% helix, 48% strand | P52434 |
| I | DNA-directed RNA polymerase III subunit RPC10 | protein | 107 | 4% helix, 34% strand | Q9Y2Y1 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 49% helix, 5% strand | P62875 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 103 | 43% helix, 27% strand | P0DPB6 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 46 | 0% helix, 30% strand | P53803 |
| M | DNA-directed RNA polymerase III subunit RPC5 | protein | 202 | 21% helix, 32% strand | Q9NVU0 |
| N | DNA-directed RNA polymerase III subunit RPC4 | protein | 146 | 16% helix, 36% strand | P05423 |
| O | DNA-directed RNA polymerase III subunit RPC3 | protein | 443 | 59% helix, 4% strand | Q9BUI4 |
| P | DNA-directed RNA polymerase III subunit RPC6 | protein | 130 | 30% helix, 2% strand | Q9H1D9 |
| Q | DNA-directed RNA polymerase III subunit RPC7 | protein | 86 | 24% helix, 0% strand | O15318 |
| R | RNA (5'-R(*CP*CP*GP*GP*GP*UP*GP*CP*UP*G)-3') | rna | 4 | — | — |
| X | Non-template DNA | dna | 22 | — | — |
| Y | Template DNA | dna | 22 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains O, P
- ZN · Zinc ion · metal · 7 copies · chains A, B, I, J, L
- MG · Magnesium ion · metal · chains A, 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 | 914 | 0.82 | 0.84 | 77 | empty |
| 2 | 1121 | 0.82 | 0.83 | 105 | empty |
| 3 | 1031 | 0.81 | 0.82 | 87 | empty |
| 4 | 875 | 0.80 | 0.83 | 105 | empty |
| 5 | 788 | 0.79 | 0.82 | 80 | empty |
Interfaces
50 interfaces between chains.
- A–B · 8778 Ų buried · 112 hydrogen bonds · protein-protein
- M–N · 4444 Ų buried · 60 hydrogen bonds · protein-protein
- O–Q · 2526 Ų buried · 16 hydrogen bonds · protein-protein
- A–O · 2234 Ų buried · 24 hydrogen bonds · protein-protein
- C–K · 2164 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7FJJ · human Pol III pre-termination complex · 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 O14802
- Every structure of UniProt Q9NW08
- Every structure of UniProt O15160
- Every structure of UniProt O75575
- Every structure of UniProt P19388
- Every structure of UniProt P61218
- Every structure of UniProt Q9Y535
- Every structure of UniProt P52434
- Every structure of UniProt Q9Y2Y1
- Every structure of UniProt P62875
- Every structure of UniProt P0DPB6
- Every structure of UniProt P53803
- Every structure of UniProt Q9NVU0
- Every structure of UniProt P05423
- Every structure of UniProt Q9BUI4
- Every structure of UniProt Q9H1D9
- Every structure of UniProt O15318
- Elsewhere: RCSB PDB 7FJJ · PDBe 7FJJ · UniProt O14802 · UniProt Q9NW08 · UniProt O15160 · UniProt O75575 · UniProt P19388 · UniProt P61218 · UniProt Q9Y535 · UniProt P52434 · UniProt Q9Y2Y1 · UniProt P62875 · UniProt P0DPB6 · UniProt P53803 · UniProt Q9NVU0 · UniProt P05423 · UniProt Q9BUI4 · UniProt Q9H1D9 · UniProt O15318
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