Research workbench
Crystal structure of response regulator ader DNA binding domain in complex with an intercistronic region
Analyse Crystal structure of response regulator ader DNA binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X5L
- Type
- protein + DNA
- Length
- 663 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ader; DNA (5'- D(P*TP*AP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*TP*AP*AP*GP*TP*GP*TP*GP*GP*AP…
- UniProt
- E1A0Z5
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ader | protein | 95 | 36% helix, 22% strand | E1A0Z5 |
| B | Ader | protein | 95 | 36% helix, 12% strand | E1A0Z5 |
| E | Ader | protein | 98 | 35% helix, 22% strand | E1A0Z5 |
| H | Ader | protein | 95 | 36% helix, 21% strand | E1A0Z5 |
| M | Ader | protein | 93 | 37% helix, 22% strand | E1A0Z5 |
| N | Ader | protein | 89 | 35% helix, 24% strand | E1A0Z5 |
| C, F | DNA (5'- D(P*TP*AP*AP*AP*GP*TP*GP*TP*GP*GP*AP*GP*TP*AP*AP*GP*TP*GP*TP*GP*GP*AP *GP*A)-3') | dna | 24 | — | — |
| D, G | DNA (5'- D(P*TP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP*AP*CP*TP*CP*CP*AP*CP*AP*CP*TP*TP *TP*A)-3') | dna | 25 | — | — |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.72 | 0.78 | 67 | empty |
| 2 | 536 | 0.66 | 0.77 | 46 | empty |
| 3 | 531 | 0.65 | 0.77 | 52 | empty |
| 4 | 335 | 0.51 | 0.72 | 41 | empty |
| 5 | 115 | 0.40 | 0.76 | 17 | empty |
Interfaces
18 interfaces between chains.
- C–D · 1100 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- F–G · 1096 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- H–C · 522 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–F · 499 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 491 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 5X5L · Crystal structure of response regulator AdeR DNA binding domain in complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
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 E1A0Z5
- Elsewhere: RCSB PDB 5X5L · PDBe 5X5L · UniProt E1A0Z5
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