Research workbench
Crystal structure of a periplasmic substrate binding protein in complex with calcium and lactate
Analyse Crystal structure of a periplasmic substrate binding protein in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZZV
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, solute-binding protein
- UniProt
- Q5SK82
- Ligands
- LAC, CA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC transporter, solute-binding protein | protein | 330 | 50% helix, 15% strand | Q5SK82 |
Ligands and binding sites
- LAC · Lactic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.69 | 0.81 | 36 | empty |
| 2 | 460 | 0.68 | 0.80 | 44 | empty |
| 3 | 164 | 0.45 | 0.75 | 20 | empty |
| 4 | 150 | 0.42 | 0.74 | 27 | empty |
| 5 | 72 | 0.31 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1380 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2ZZV · Crystal Structure of a Periplasmic Substrate Binding Protein in Complex with Calcium and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SK82 · AlphaFold monomer V2.0 prediction for lactate-binding periplasmic protein TTHA0766… · a predicted model of the same protein · 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 Q5SK82
- Elsewhere: RCSB PDB 2ZZV · PDBe 2ZZV · UniProt Q5SK82
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