Research workbench
Crystal structure of a trap periplasmic solute binding protein from sulfitobacter sp. nas-14.1, target efi-510292, with bound alpha-D- manuronate
Analyse Crystal structure of a trap periplasmic solute binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OVP
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C4-dicarboxylate transport system substrate-binding protein
- UniProt
- A3T0D1
- Ligands
- MAV
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C4-dicarboxylate transport system substrate-binding protein | protein | 308 | 48% helix, 20% strand | A3T0D1 |
| B | C4-dicarboxylate transport system substrate-binding protein | protein | 302 | 51% helix, 20% strand | A3T0D1 |
Ligands and binding sites
- MAV · alpha-D-mannopyranuronic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.74 | 0.78 | 79 | empty |
| 2 | 120 | 0.57 | 0.84 | 32 | MAV |
| 3 | 127 | 0.55 | 0.82 | 29 | MAV |
| 4 | 108 | 0.37 | 0.74 | 18 | empty |
| 5 | 86 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 4OVP · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp.… · the same entry in another collection · chain A against A, TM-score 1.00
- A3T0D1 · AlphaFold monomer V2.0 prediction for solute-binding protein NAS141_03721 (A3T0D1) · a predicted model of the same protein · chain B 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 A3T0D1
- Elsewhere: RCSB PDB 4OVP · PDBe 4OVP · UniProt A3T0D1
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