Research workbench
Crystal structure of a trap periplasmic solute binding protein from citrobacter koseri (CKO_04899, target efi-510094) with bound D- glucuronate
Analyse Crystal structure of a trap periplasmic solute binding protein from citrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X04
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Solute binding protein
- UniProt
- A8AR30
- Ligands
- BDP, MG, CL
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Solute binding protein | protein | 301 | 50% helix, 19% strand | A8AR30 |
Ligands and binding sites
- BDP · beta-D-glucopyranuronic acid · sugar · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D, C
- CL · Chloride ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.74 | 0.77 | 87 | empty |
| 2 | 331 | 0.66 | 0.81 | 33 | empty |
| 3 | 163 | 0.65 | 0.86 | 33 | BDP, CL |
| 4 | 282 | 0.65 | 0.82 | 54 | BDP, CL |
| 5 | 90 | 0.63 | 0.90 | 22 | BDP, CL |
Interfaces
4 interfaces between chains.
- A–D · 1006 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 186 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 4X04 · CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CITROBACTER KOSERI… · 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 A8AR30
- Elsewhere: RCSB PDB 4X04 · PDBe 4X04 · UniProt A8AR30
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