MolNFT v1 · #57090 · protein
Crystal structure of a periplasmic substrate binding protein in complex with lactate
2ZZX · ABC transporter, solute-binding protein: “Crystal structure of a periplasmic substrate binding protein in complex with lactate”. X-ray diffraction, 3 ligands (LAC, CA, PO4), 11 pockets (best druggability 0.78). MolNFT v1 #57090 on…
- PDB
- 2ZZX
- Type
- protein
- Length
- 1,313 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, solute-binding protein
- UniProt
- Q5SK82
- Ligands
- LAC, CA, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, solute-binding protein | protein | 330 | 50% helix, 15% strand | Q5SK82 |
| B | ABC transporter, solute-binding protein | protein | 328 | 49% helix, 15% strand | Q5SK82 |
| C | ABC transporter, solute-binding protein | protein | 326 | 51% helix, 15% strand | Q5SK82 |
| D | ABC transporter, solute-binding protein | protein | 329 | 49% helix, 15% strand | Q5SK82 |
Ligands and binding sites
- LAC · Lactic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains C
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.78 | 0.81 | 75 | empty |
| 2 | 1124 | 0.76 | 0.78 | 97 | empty |
| 3 | 473 | 0.70 | 0.80 | 44 | empty |
| 4 | 375 | 0.69 | 0.81 | 33 | empty |
| 5 | 88 | 0.58 | 0.87 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1399 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1382 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 295 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2ZZX · Crystal Structure of a Periplasmic Substrate Binding Protein in Complex with Lactate · the same entry in another collection · chain D against D, TM-score 1.00
- Q5SK82 · AlphaFold monomer V2.0 prediction for lactate-binding periplasmic protein TTHA0766… · a predicted model of the same protein · chain D 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 2ZZX · PDBe 2ZZX · UniProt Q5SK82
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