MolNFT v1 · #69071 · protein
Crystal structure of putative sugar binding protein (YP_001299726.1) from bacteroides vulgatus atcc 8482 at 1.90 a resolution
3KEZ: “Crystal structure of putative sugar binding protein (YP_001299726.1) from bacteroides vulgatus atcc 8482 at…”. X-ray diffraction, 2 ligands (CA, PO4), 4 pockets (best druggability 0.82). MolNFT v1 #69071 on GenesisL1: 3D structure…
- PDB
- 3KEZ
- Type
- protein
- Length
- 895 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sugar binding protein
- UniProt
- A6L340
- Ligands
- CA, PO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sugar binding protein | protein | 447 | 48% helix, 8% strand | A6L340 |
| B | Putative sugar binding protein | protein | 448 | 48% helix, 7% strand | A6L340 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.82 | 0.83 | 102 | EDO |
| 2 | 422 | 0.67 | 0.79 | 29 | EDO |
| 3 | 131 | 0.42 | 0.75 | 18 | EDO |
| 4 | 113 | 0.42 | 0.76 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 844 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 3KEZ · Crystal structure of Putative sugar binding protein (YP_001299726.1) from Bacteroides… · 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 A6L340
- Elsewhere: RCSB PDB 3KEZ · PDBe 3KEZ · UniProt A6L340
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