Research workbench
Crystallographic structure of the molybdate-binding protein of xanthomonas citri at 1.7 ang resolution bound to molybdate
Analyse Crystallographic structure of the molybdate-binding protein of xanthomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H5Y
- Type
- protein
- Length
- 697 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdate-binding periplasmic protein
- UniProt
- Q8PHA1
- Ligands
- SO4, MOO
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Molybdate-binding periplasmic protein | protein | 232 | 41% helix, 24% strand | Q8PHA1 |
| B | Molybdate-binding periplasmic protein | protein | 233 | 42% helix, 24% strand | Q8PHA1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- MOO · Molybdate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.66 | 0.75 | 83 | SO4 |
| 2 | 98 | 0.48 | 0.81 | 30 | empty |
| 3 | 133 | 0.44 | 0.76 | 19 | empty |
| 4 | 101 | 0.33 | 0.73 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 568 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2H5Y · Crystallographic structure of the Molybdate-Binding Protein of Xanthomonas citri at 1.7… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PHA1 · AlphaFold monomer V2.0 prediction for molybdate-binding protein moda (Q8PHA1) · a predicted model of the same protein · 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 Q8PHA1
- Elsewhere: RCSB PDB 2H5Y · PDBe 2H5Y · UniProt Q8PHA1
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