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The crystal structure of a solute-binding protein from anabaena variabilis atcc 29413 in complex with pyruvic acid
Analyse The crystal structure of a solute-binding protein from anabaena variabilis atcc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RV5
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino ACID/AMIDE ABC transporter substrate-binding protein, haat family
- UniProt
- Q3MFZ5
- Ligands
- PYR, MG
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amino ACID/AMIDE ABC transporter substrate-binding protein, haat family | protein | 364 | 46% helix, 20% strand | Q3MFZ5 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.68 | 0.77 | 53 | empty |
| 2 | 89 | 0.52 | 0.83 | 21 | FMT |
| 3 | 141 | 0.47 | 0.77 | 30 | empty |
| 4 | 129 | 0.42 | 0.76 | 24 | empty |
| 5 | 75 | 0.42 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 661 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, engineered).
Compared structures
- 4RV5 · The crystal structure of a solute-binding protein from Anabaena variabilis ATCC 29413 in… · 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 Q3MFZ5
- Elsewhere: RCSB PDB 4RV5 · PDBe 4RV5 · UniProt Q3MFZ5
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