MolNFT v1 · #190698 · protein + DNA + RNA
The cryo-EM structure of an alpa-loading complex
7XYA · DNA-directed RNA polymerase subunit alpha: “The cryo-EM structure of an alpa-loading complex”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.84). MolNFT v1 #190698 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7XYA
- Type
- protein + DNA + RNA
- Length
- 3,605 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
- O52760, Q51561, Q9HWC9, Q9HTM1, P26480, A0A2R3ITY7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 20% helix, 38% strand | O52760 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 209 | 20% helix, 35% strand | O52760 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1190 | 31% helix, 22% strand | Q51561 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1338 | 36% helix, 16% strand | Q9HWC9 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 67 | 57% helix, 0% strand | Q9HTM1 |
| F | RNA polymerase sigma factor rpod | protein | 302 | 78% helix, 1% strand | P26480 |
| N | Nontemplate strand DNA | dna | 58 | — | — |
| R | RNA | rna | 10 | — | — |
| T | Template strand DNA | dna | 58 | — | — |
| G | Alpa | protein | 158 | 77% helix, 0% strand | A0A2R3ITY7 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D, 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 | 951 | 0.84 | 0.85 | 96 | empty |
| 2 | 968 | 0.83 | 0.84 | 83 | empty |
| 3 | 1149 | 0.82 | 0.83 | 139 | empty |
| 4 | 711 | 0.79 | 0.84 | 111 | empty |
| 5 | 377 | 0.79 | 0.89 | 50 | empty |
Interfaces
23 interfaces between chains.
- C–D · 7526 Ų buried · 78 hydrogen bonds · protein-protein
- N–T · 1987 Ų buried · 176 hydrogen bonds · nucleic-nucleic
- A–B · 1807 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1573 Ų buried · 14 hydrogen bonds · protein-protein
- F–N · 1369 Ų buried · 23 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7XYA · The cryo-EM structure of an AlpA-loading complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q51561 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q51561) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P26480 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpod (P26480) · a predicted model of the same protein · chain F against A, TM-score 0.93
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 O52760
- Every structure of UniProt Q51561
- Every structure of UniProt Q9HWC9
- Every structure of UniProt Q9HTM1
- Every structure of UniProt P26480
- Every structure of UniProt A0A2R3ITY7
- Elsewhere: RCSB PDB 7XYA · PDBe 7XYA · UniProt O52760 · UniProt Q51561 · UniProt Q9HWC9 · UniProt Q9HTM1 · UniProt P26480 · UniProt A0A2R3ITY7
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