Research workbench
A model of the ternary complex formed between mara, the alpha-ctd of RNA polymerase and DNA
Analyse A model of the ternary complex formed between mara, the alpha-ctd of RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XS9
- Type
- protein + DNA
- Length
- 250 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*C P*AP*T)-3'…
- EC
- 2.7.7.6
- UniProt
- P0ACH5, P0A7Z4
- Pockets
- 4 · best druggability 0.70
Structure
solution nmr · 4 distinct chains · 44% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*C P*AP*T)-3' | dna | 20 | — | — |
| C | 5'-D(P*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*A P*TP*C)-3' | dna | 20 | — | — |
| A | Multiple antibiotic resistance protein mara | protein | 129 | 49% helix, 0% strand | P0ACH5 |
| D | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 81 | 36% helix, 0% strand | P0A7Z4 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.70 | 0.86 | 24 | empty |
| 2 | 181 | 0.50 | 0.78 | 27 | empty |
| 3 | 69 | 0.34 | 0.76 | 14 | empty |
| 4 | 53 | 0.26 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 956 Ų buried · 115 hydrogen bonds · nucleic-nucleic
- C–A · 721 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–A · 718 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 630 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1XS9 · A model of the ternary complex formed between mara, the alpha-ctd of RNA polymerase and… · the same entry in another collection · chain B against B, TM-score 1.00
- P0ACH5 · AlphaFold monomer V2.0 prediction for multiple antibiotic resistance protein mara (P0ACH5) · a predicted model of the same protein · chain A 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 P0ACH5
- Every structure of UniProt P0A7Z4
- Elsewhere: RCSB PDB 1XS9 · PDBe 1XS9 · UniProt P0ACH5 · UniProt P0A7Z4
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