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Crystal structure of a periplasmic binding protein (BMA2936) from burkholderia mallei at 1.80 a resolution
Analyse Crystal structure of a periplasmic binding protein (BMA2936) from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I09
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic branched-chain amino acid-binding protein
- UniProt
- Q62FT5
- Ligands
- AAE
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic branched-chain amino acid-binding protein | protein | 375 | 43% helix, 22% strand | Q62FT5 |
Ligands and binding sites
- AAE · Acetoacetic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- CIT · Citric acid · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 632 | 0.63 | 0.74 | 65 | EDO |
| 2 | 118 | 0.42 | 0.76 | 23 | EDO |
| 3 | 98 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 131 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 28 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3I09 · Crystal structure of a periplasmic binding protein (BMA2936) from burkholderia mallei at… · 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 Q62FT5
- Elsewhere: RCSB PDB 3I09 · PDBe 3I09 · UniProt Q62FT5
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