MolNFT v1 · #116144 · protein + DNA
Crystal structure of ARAR(DBD) in complex with operator ORX1
5D4S · Arabinose metabolism transcriptional repressor: “Crystal structure of ARAR(DBD) in complex with operator ORX1”. X-ray diffraction, 3 pockets (best druggability 0.76). MolNFT v1 #116144 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5D4S
- Type
- protein + DNA
- Length
- 195 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arabinose metabolism transcriptional repressor; DNA (5'…
- UniProt
- P96711
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arabinose metabolism transcriptional repressor | protein | 70 | 47% helix, 13% strand | P96711 |
| B | Arabinose metabolism transcriptional repressor | protein | 83 | 41% helix, 12% strand | P96711 |
| T | DNA (5'- D(*TP*AP*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*TP*AP*TP*GP*TP*AP*TP*T)- 3') | dna | 21 | — | — |
| U | DNA (5'- D(*AP*AP*AP*TP*AP*CP*AP*TP*AP*CP*GP*TP*AP*CP*AP*AP*AP*TP*AP*TP*T)- 3') | dna | 21 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.76 | 0.83 | 52 | empty |
| 2 | 185 | 0.45 | 0.75 | 19 | empty |
| 3 | 55 | 0.27 | 0.74 | 12 | empty |
Interfaces
6 interfaces between chains.
- T–U · 922 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- B–U · 530 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–T · 514 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–U · 472 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–T · 467 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5D4S · Crystal Structure of AraR(DBD) in complex with operator ORX1 · 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 0.95
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 5D4S · PDBe 5D4S · UniProt P96711
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