MolNFT v1 · #159379 · protein
Crystal structure of periplasmic binding protein xoxj from methylobacterium extorquens AM1
6ONP: “Crystal structure of periplasmic binding protein xoxj from methylobacterium extorquens AM1”. X-ray diffraction, 1 pocket (best druggability 0.58). MolNFT v1 #159379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ONP
- Type
- protein
- Length
- 211 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding protein xoxj
- UniProt
- C5B122
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic binding protein xoxj | protein | 211 | 34% helix, 23% strand | C5B122 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.58 | 0.77 | 34 | EDO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ONP · Crystal structure of periplasmic binding protein XoxJ from Methylobacterium extorquens AM1 · 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 C5B122
- Elsewhere: RCSB PDB 6ONP · PDBe 6ONP · UniProt C5B122
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