Research workbench
Crystal structure of metal-dependent hydrolase ybey from E. COLI, pfam UPF0054
Analyse Crystal structure of metal-dependent hydrolase ybey from E. COLI, pfam UPF0054 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XM5
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical UPF0054 protein ybey
- UniProt
- P0A898
- Ligands
- NI
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Hypothetical UPF0054 protein ybey | protein | 152 | 45% helix, 20% strand | P0A898 |
| C | Hypothetical UPF0054 protein ybey | protein | 148 | 46% helix, 19% strand | P0A898 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.80 | 0.93 | 32 | empty |
| 2 | 295 | 0.76 | 0.88 | 37 | empty |
| 3 | 660 | 0.74 | 0.80 | 59 | NI |
| 4 | 236 | 0.58 | 0.79 | 33 | empty |
| 5 | 175 | 0.55 | 0.80 | 30 | NI |
Interfaces
4 interfaces between chains.
- B–C · 879 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 852 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 199 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1XM5 · Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A898 · AlphaFold monomer V2.0 prediction for endoribonuclease ybey (P0A898) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0A898
- Elsewhere: RCSB PDB 1XM5 · PDBe 1XM5 · UniProt P0A898
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