MolNFT v1 · #139122 · protein + DNA
Crystal structure of response regulator ader DNA binding domain in complex with an intercistronic region
5X5L: “Crystal structure of response regulator ader DNA binding domain in complex with an intercistronic region”. X-ray diffraction, 11 pockets (best druggability 0.72). MolNFT v1 #139122 on GenesisL1: 3D structure, binding sites and…
- 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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