MolNFT v1 · #90360 · protein + DNA
Crystal structure of ARAR(DBD) in complex with operator ORR3
4EGZ · Arabinose metabolism transcriptional repressor: “Crystal structure of ARAR(DBD) in complex with operator ORR3”. X-ray diffraction, 2 pockets (best druggability 0.61). MolNFT v1 #90360 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4EGZ
- Type
- protein + DNA
- Length
- 206 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arabinose metabolism transcriptional repressor…
- UniProt
- P96711
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arabinose metabolism transcriptional repressor | protein | 81 | 43% helix, 16% strand | P96711 |
| B | Arabinose metabolism transcriptional repressor | protein | 83 | 42% helix, 11% strand | P96711 |
| T | 5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*TP*AP*CP*AP*TP *TP*TP*T)-3' | dna | 21 | — | — |
| U | 5'-D(*TP*AP*AP*AP*AP*TP*GP*TP*AP*TP*AP*CP*GP*GP*AP*CP*AP*AP *AP*TP*T)-3' | dna | 21 | — | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 5 copies · chains A, U, B, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.61 | 0.76 | 49 | ACT |
| 2 | 93 | 0.41 | 0.78 | 15 | empty |
Interfaces
5 interfaces between chains.
- T–U · 900 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- B–U · 577 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–U · 543 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–T · 536 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–T · 461 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4EGZ · Crystal Structure of AraR(DBD) in complex with operator ORR3 · the same entry in another collection · chain A against A, TM-score 1.00
- P96711 · AlphaFold monomer V2.0 prediction for arabinose metabolism transcriptional repressor… · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P96711
- Elsewhere: RCSB PDB 4EGZ · PDBe 4EGZ · UniProt P96711
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