MolNFT v1 · #176667 · protein + DNA + RNA
RNA polymerase III ec complex in post-translocation state
7DU2 · DNA-directed RNA polymerase III subunit RPC1: “RNA polymerase III ec complex in post-translocation state”. Electron microscopy, 3 ligands (SF4, ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #176667 on GenesisL1: 3D…
- PDB
- 7DU2
- Type
- protein + DNA + RNA
- Length
- 4,546 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, Q9Y535, P0DPB6, P53803, Q9H1D9, P19388, P61218, P52434, P62875, Q9BUI4, O15318, O75575, Q9NVU0, P05423, Q9Y2Y1
- Ligands
- SF4, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 20 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 | 1293 | 36% helix, 13% strand | O14802 |
| B | DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6) | protein | 1044 | 26% helix, 19% strand | Q9NW08 |
| C | DNA-directed RNA polymerases I and III subunit RPAC1 | protein | 330 | 22% helix, 24% strand | O15160 |
| G | DNA-directed RNA polymerase III subunit RPC8 | protein | 166 | 8% helix, 36% strand | Q9Y535 |
| K | DNA-directed RNA polymerases I and III subunit RPAC2 | protein | 103 | 40% helix, 22% strand | P0DPB6 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 27% strand | P53803 |
| P | DNA-directed RNA polymerase III subunit RPC6 | protein | 130 | 30% helix, 2% strand | Q9H1D9 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 194 | 30% helix, 18% strand | P19388 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 76 | 33% helix, 17% strand | P61218 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 122 | 0% helix, 48% strand | P52434 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 64 | 45% helix, 2% strand | P62875 |
| O | DNA-directed RNA polymerase III subunit RPC3 | protein | 443 | 59% helix, 4% strand | Q9BUI4 |
| Q | DNA-directed RNA polymerase III subunit RPC7 | protein | 86 | 24% helix, 0% strand | O15318 |
| D | DNA-directed RNA polymerase III subunit RPC9 | protein | 122 | 61% helix, 2% strand | O75575 |
| M | DNA-directed RNA polymerase III subunit RPC5 | protein | 154 | 10% helix, 16% strand | Q9NVU0 |
| N | DNA-directed RNA polymerase III subunit RPC4 | protein | 92 | 12% helix, 39% strand | P05423 |
| I | DNA-directed RNA polymerase III subunit RPC10 | protein | 47 | 0% helix, 4% strand | Q9Y2Y1 |
| X | DNA (5'-D(P*GP*TP*CP*TP*GP*AP*TP*CP*TP*CP*GP*GP*AP*A)-3') | dna | 14 | — | — |
| Y | DNA (5'- D(P*TP*TP*CP*CP*GP*AP*GP*AP*TP*CP*AP*GP*AP*CP*GP*AP*GP*AP*T)-3') | dna | 19 | — | — |
| R | RNA (5'-R(P*AP*UP*C)-3') | rna | 3 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains P, O
- ZN · Zinc ion · metal · 6 copies · chains A, B, L, J, I
- MG · Magnesium ion · metal · chains A
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 | 888 | 0.83 | 0.85 | 97 | empty |
| 2 | 947 | 0.81 | 0.83 | 100 | empty |
| 3 | 1101 | 0.80 | 0.81 | 112 | empty |
| 4 | 816 | 0.79 | 0.82 | 54 | empty |
| 5 | 1076 | 0.79 | 0.81 | 113 | MG |
Interfaces
47 interfaces between chains.
- A–B · 8524 Ų buried · 103 hydrogen bonds · protein-protein
- O–Q · 2525 Ų buried · 16 hydrogen bonds · protein-protein
- M–N · 2152 Ų buried · 33 hydrogen bonds · protein-protein
- C–K · 2127 Ų buried · 15 hydrogen bonds · protein-protein
- G–D · 2033 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7DU2 · RNA polymerase III EC complex in post-translocation state · 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 Q9Y535
- Every structure of UniProt P0DPB6
- Every structure of UniProt P53803
- Every structure of UniProt Q9H1D9
- Every structure of UniProt P19388
- Every structure of UniProt P61218
- Every structure of UniProt P52434
- Every structure of UniProt P62875
- Every structure of UniProt Q9BUI4
- Every structure of UniProt O15318
- Every structure of UniProt O75575
- Every structure of UniProt Q9NVU0
- Every structure of UniProt P05423
- Every structure of UniProt Q9Y2Y1
- Elsewhere: RCSB PDB 7DU2 · PDBe 7DU2 · UniProt O14802 · UniProt Q9NW08 · UniProt O15160 · UniProt Q9Y535 · UniProt P0DPB6 · UniProt P53803 · UniProt Q9H1D9 · UniProt P19388 · UniProt P61218 · UniProt P52434 · UniProt P62875 · UniProt Q9BUI4 · UniProt O15318 · UniProt O75575 · UniProt Q9NVU0 · UniProt P05423 · UniProt Q9Y2Y1
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