Research workbench
Crystal structure of the murine aum (phosphoglycolate phosphatase) capping domain as a fusion protein with the catalytic core domain of murine chronophin (pyridoxal phosphate phosphatase)
Analyse Crystal structure of the murine aum (phosphoglycolate phosphatase) capping… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BKM
- Type
- protein
- Length
- 1,216 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphate phosphatase, phosphoglycolate phosphatase, pyridoxal phosphate…
- EC
- 3.1.3.3, 3.1.3.74, 3.1.3.18
- UniProt
- P60487, Q8CHP8
- Ligands
- MG, NO3
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyridoxal phosphate phosphatase, phosphoglycolate phosphatase, pyridoxal phosphate phosphatase (EC 3.1.3.3, 3.1.3.74, 3.1.3.18) | protein | 304 | 40% helix, 20% strand | P60487, Q8CHP8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.73 | 0.81 | 62 | MG |
| 2 | 514 | 0.72 | 0.81 | 66 | NO3 |
| 3 | 780 | 0.71 | 0.77 | 80 | MG |
| 4 | 400 | 0.71 | 0.82 | 40 | MG |
| 5 | 66 | 0.58 | 0.89 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1592 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1505 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 341 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 183 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4BKM · Crystal structure of the murine AUM (phosphoglycolate phosphatase) capping domain as a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CHP8 · AlphaFold monomer V2.0 prediction for glycerol-3-phosphate phosphatase (Q8CHP8) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P60487 · AlphaFold monomer V2.0 prediction for pyridoxal phosphate phosphatase (P60487) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P60487
- Every structure of UniProt Q8CHP8
- Elsewhere: RCSB PDB 4BKM · PDBe 4BKM · UniProt P60487 · UniProt Q8CHP8
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