MolNFT v1 · #175966 · protein + DNA
Cryoem structure of GP45-dependent transcription activation complex
7D7D · DNA-directed RNA polymerase subunit alpha: “Cryoem structure of GP45-dependent transcription activation complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #175966 on GenesisL1: 3D…
- PDB
- 7D7D
- Type
- protein + DNA
- Length
- 4,170 residues
- Chains
- 12
- Method
- electron microscopy
- 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
- U9ZUN7, A0A080FHH4, D7Y6A2, P13338, A0A070UPX4, P04525
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 19% helix, 33% strand | U9ZUN7 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 20% helix, 33% strand | U9ZUN7 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 21% strand | A0A080FHH4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 34% helix, 15% strand | D7Y6A2 |
| T | DNA (template strand) | dna | 46 | — | — |
| F | GP55 | protein | 137 | 68% helix, 0% strand | — |
| N | DNA (nontemplate strand) | dna | 48 | — | — |
| K | RNA polymerase-associated protein GP33 | protein | 71 | 59% helix, 0% strand | P13338 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 71 | 56% helix, 0% strand | A0A070UPX4 |
| G, H, I | DNA polymerase clamp | protein | 228 | 18% helix, 42% strand | P04525 |
Ligands and binding sites
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 | 944 | 0.84 | 0.85 | 101 | empty |
| 2 | 895 | 0.83 | 0.85 | 117 | empty |
| 3 | 962 | 0.83 | 0.84 | 138 | empty |
| 4 | 119 | 0.79 | 0.97 | 26 | empty |
| 5 | 1082 | 0.79 | 0.81 | 89 | empty |
Interfaces
29 interfaces between chains.
- C–D · 7636 Ų buried · 85 hydrogen bonds · protein-protein
- T–N · 1873 Ų buried · 215 hydrogen bonds · nucleic-nucleic
- A–B · 1783 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1659 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1548 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7D7D · CryoEM structure of gp45-dependent transcription activation complex · the same entry in another collection · chain A against A, 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 U9ZUN7
- Every structure of UniProt A0A080FHH4
- Every structure of UniProt D7Y6A2
- Every structure of UniProt P13338
- Every structure of UniProt A0A070UPX4
- Every structure of UniProt P04525
- Elsewhere: RCSB PDB 7D7D · PDBe 7D7D · UniProt U9ZUN7 · UniProt A0A080FHH4 · UniProt D7Y6A2 · UniProt P13338 · UniProt A0A070UPX4 · UniProt P04525
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