Research workbench
RNA polymerase-GFH1 complex (crystal type 1)
Analyse RNA polymerase-GFH1 complex (crystal type 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AOH
- Type
- protein + DNA + RNA
- Length
- 9,386 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SJG6
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 13 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 21% helix, 39% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1106 | 27% helix, 24% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1349 | 38% helix, 15% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 93 | 46% helix, 4% strand | Q8RQE7 |
| F, K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 22% helix, 39% strand | Q5SHR6 |
| H | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1103 | 27% helix, 23% strand | Q8RQE9 |
| I | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1289 | 40% helix, 13% strand | Q8RQE8 |
| J | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 92 | 47% helix, 4% strand | Q8RQE7 |
| M | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1105 | 27% helix, 24% strand | Q8RQE9 |
| N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1351 | 38% helix, 15% strand | Q8RQE8 |
| P | DNA (5'- D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*AP*CP*CP*GP*CP* CP*GP*CP*AP*T)-3') | dna | 6 | — | — |
| Q | RNA (5'- R(*CP*CP*CP*CP*GP*GP*AP*AP*GP*AP*UP*CP*AP*UP*CP*UP*UP*CP*CP*GP*GP*GP* GP*GP*AP*U*GP*CP*GP*GP*CP*GP*G)-3') | rna | 7 | — | — |
| X, Y, Z | Anti-cleavage anti-grea transcription factor GFH1 | protein | 152 | 41% helix, 22% strand | Q5SJG6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains D, I, N
- MG · Magnesium ion · metal · 3 copies · chains D, Q, I, N
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 | 760 | 0.87 | 0.90 | 103 | empty |
| 2 | 1146 | 0.87 | 0.88 | 123 | empty |
| 3 | 682 | 0.86 | 0.90 | 76 | empty |
| 4 | 735 | 0.85 | 0.89 | 94 | empty |
| 5 | 951 | 0.85 | 0.86 | 142 | MG |
Interfaces
42 interfaces between chains.
- M–N · 8654 Ų buried · 97 hydrogen bonds · protein-protein
- H–I · 8474 Ų buried · 97 hydrogen bonds · protein-protein
- C–D · 8296 Ų buried · 103 hydrogen bonds · protein-protein
- D–E · 2380 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 2377 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3AOH · RNA polymerase-Gfh1 complex (Crystal type 1) · the same entry in another collection · chain D against D, 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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SJG6
- Elsewhere: RCSB PDB 3AOH · PDBe 3AOH · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SJG6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.