Research workbench
Structure of mycobacterium smegmatis held protein in complex with RNA polymerase core - state II, primary channel engaged and active site interfering
Analyse Structure of mycobacterium smegmatis held protein in complex with RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YYS
- Type
- protein
- Length
- 3,597 residues
- Chains
- 6
- 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, 3.6.4.12
- UniProt
- A0QSL8, P60281, A0QS66, A0QWT1, A0QUE0
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 21% helix, 33% strand | A0QSL8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 18% helix, 33% strand | A0QSL8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1089 | 22% helix, 26% strand | P60281 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1278 | 40% helix, 13% strand | A0QS66 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 42% helix, 5% strand | A0QWT1 |
| H | RNA polymerase-associated transcription factor held (EC 3.6.4.12) | protein | 690 | 39% helix, 11% strand | A0QUE0 |
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 | 1021 | 0.82 | 0.83 | 103 | empty |
| 2 | 659 | 0.81 | 0.86 | 84 | empty |
| 3 | 1101 | 0.79 | 0.81 | 115 | empty |
| 4 | 661 | 0.78 | 0.83 | 83 | empty |
| 5 | 860 | 0.78 | 0.81 | 65 | empty |
Interfaces
10 interfaces between chains.
- C–D · 7746 Ų buried · 75 hydrogen bonds · protein-protein
- D–H · 3970 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2245 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2180 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2041 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6YYS · Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core… · the same entry in another collection · chain H against H, TM-score 1.00
- P60281 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P60281) · a predicted model of the same protein · chain C against A, TM-score 0.98
- A0QSL8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (A0QSL8) · a predicted model of the same protein · chain A against A, TM-score 0.96
- A0QWT1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (A0QWT1) · a predicted model of the same protein · chain E against A, TM-score 0.92
- A0QS66 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (A0QS66) · 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 A0QSL8
- Every structure of UniProt P60281
- Every structure of UniProt A0QS66
- Every structure of UniProt A0QWT1
- Every structure of UniProt A0QUE0
- Elsewhere: RCSB PDB 6YYS · PDBe 6YYS · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QUE0
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