MolNFT v1 · #118363 · protein
RNA polymerase model placed by molecular replacement into X-ray diffraction MAP of DNA-bound RNA polymerase-sigma 54 holoenzyme complex.
5EZK · DNA-directed RNA polymerase subunit alpha: “RNA polymerase model placed by molecular replacement into X-ray diffraction MAP of DNA-bound RNA…”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #118363 on GenesisL1…
- PDB
- 5EZK
- Type
- protein
- Length
- 3,129 residues
- Chains
- 5
- 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
- P0A7Z6, P0A8V4, P0A8T8, P0A800
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 323 | 27% helix, 24% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 19% helix, 34% strand | P0A7Z6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1335 | 30% helix, 17% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1160 | 40% helix, 10% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 66% helix, 0% strand | P0A800 |
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 | 966 | 0.88 | 0.89 | 171 | empty |
| 2 | 1156 | 0.84 | 0.85 | 160 | empty |
| 3 | 1135 | 0.83 | 0.85 | 154 | empty |
| 4 | 385 | 0.81 | 0.90 | 68 | empty |
| 5 | 949 | 0.80 | 0.82 | 115 | empty |
Interfaces
8 interfaces between chains.
- C–D · 3334 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 573 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 501 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 380 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5EZK · RNA polymerase model placed by Molecular replacement into X-ray diffraction map of… · the same entry in another collection · chain E against E, TM-score 1.00
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P0A7Z6
- Every structure of UniProt P0A8V4
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 5EZK · PDBe 5EZK · UniProt P0A7Z6 · UniProt P0A8V4 · UniProt P0A8T8 · UniProt P0A800
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