Research workbench
Crystal structure of holo-viup
Analyse Crystal structure of holo-viup in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R5T
- Type
- protein
- Length
- 296 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein
- UniProt
- Q9RCF6
- Ligands
- VBN, FE
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein | protein | 296 | 36% helix, 19% strand | Q9RCF6 |
Ligands and binding sites
- VBN · (4S,5R)-N-{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-N-[3-({[(4S,5R)-2-(2,3-dihydroxyphenyl)-5-met hyl-4,5-dihydro-1,3-oxazol-4-yl]carbonyl}amino)propyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- MOH · Methanol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.32 | 0.76 | 13 | FE |
Compared structures
- 3R5T · Crystal structure of holo-ViuP · 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 Q9RCF6
- Elsewhere: RCSB PDB 3R5T · PDBe 3R5T · UniProt Q9RCF6
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