MolNFT v1 · #92081 · protein
Crystal structure of the nucleotide-binding domain of a dipeptide ABC transporter
4FWI · ABC-type DIPEPTIDE/OLIGOPEPTIDE/NICKEL transport system…: “Crystal structure of the nucleotide-binding domain of a dipeptide ABC transporter”. X-ray diffraction, 3 ligands (SF4, ATP, MG), 2 pockets (best druggability 0.60). MolNFT…
- PDB
- 4FWI
- Type
- protein
- Length
- 310 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type DIPEPTIDE/OLIGOPEPTIDE/NICKEL transport system, ATPase component
- UniProt
- Q8RDH4
- Ligands
- SF4, ATP, MG
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ABC-type DIPEPTIDE/OLIGOPEPTIDE/NICKEL transport system, ATPase component | protein | 310 | 35% helix, 23% strand | Q8RDH4 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains B
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.60 | 0.81 | 32 | empty |
| 2 | 65 | 0.53 | 0.86 | 19 | empty |
Compared structures
- 4FWI · Crystal structure of the nucleotide-binding domain of a dipeptide ABC transporter · the same entry in another collection · chain B against B, TM-score 1.00
- Q8RDH4 · AlphaFold monomer V2.0 prediction for dipeptide transport ATP-binding protein dppd… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8RDH4
- Elsewhere: RCSB PDB 4FWI · PDBe 4FWI · UniProt Q8RDH4
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