MolNFT v1 · #70760 · protein
Molecular model of escherichia COLI core RNA polymerase
3LU0 · DNA-directed RNA polymerase subunit alpha: “Molecular model of escherichia COLI core RNA polymerase”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #70760 on GenesisL1: 3D structure, binding…
- PDB
- 3LU0
- Type
- protein
- Length
- 3,258 residues
- Chains
- 5
- 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
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 25% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 235 | 15% helix, 29% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1335 | 24% helix, 16% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1364 | 26% helix, 12% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 44% helix, 3% strand | P0A800 |
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 | 1027 | 0.84 | 0.85 | 117 | empty |
| 2 | 756 | 0.84 | 0.87 | 74 | empty |
| 3 | 954 | 0.81 | 0.82 | 84 | empty |
| 4 | 772 | 0.77 | 0.81 | 72 | empty |
| 5 | 598 | 0.76 | 0.82 | 68 | empty |
Interfaces
8 interfaces between chains.
- C–D · 8521 Ų buried · 88 hydrogen bonds · protein-protein
- A–C · 2235 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 2183 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1965 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1761 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3LU0 · Molecular model of Escherichia coli core RNA polymerase · the same entry in another collection · chain B against B, TM-score 1.00
- 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 0.87
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain D against A, TM-score 0.79
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
- Elsewhere: RCSB PDB 3LU0 · PDBe 3LU0 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800
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