MolNFT v1 · #67908 · protein + DNA
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
3IYD · DNA-directed RNA polymerase subunit alpha: “Three-dimensional EM structure of an intact activator-dependent transcription initiation complex”. Electron microscopy, 1 ligand (CMP), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 3IYD
- Type
- protein + DNA
- Length
- 4,181 residues
- Chains
- 10
- 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
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, P0ACJ8
- Ligands
- CMP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 9 distinct chains · 22% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 322 | 20% helix, 13% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 235 | 14% helix, 18% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1089 | 14% helix, 15% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1368 | 21% helix, 10% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 26% helix, 3% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 479 | 46% helix, 0% strand | P00579 |
| G, H | Catabolite gene activator | protein | 201 | 32% helix, 24% strand | P0ACJ8 |
| I | DNA (98-mer) | dna | 98 | — | — |
| J | DNA (98-mer) | dna | 98 | — | — |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains G, H
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 | 1187 | 0.89 | 0.90 | 136 | empty |
| 2 | 835 | 0.83 | 0.85 | 95 | empty |
| 3 | 1138 | 0.82 | 0.84 | 111 | empty |
| 4 | 1011 | 0.81 | 0.82 | 107 | empty |
| 5 | 218 | 0.80 | 0.94 | 40 | empty |
Interfaces
29 interfaces between chains.
- C–D · 7999 Ų buried · 90 hydrogen bonds · protein-protein
- I–J · 3095 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- D–E · 2457 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2166 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 2156 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3IYD · Three-dimensional EM structure of an intact activator-dependent transcription initiation… · the same entry in another collection · chain I against I, TM-score 1.00
- P0ACJ8 · AlphaFold monomer V2.0 prediction for camp-activated global transcriptional regulator crp… · a predicted model of the same protein · chain H against A, TM-score 0.89
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Every structure of UniProt P0ACJ8
- Elsewhere: RCSB PDB 3IYD · PDBe 3IYD · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt P0ACJ8
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