MolNFT v1 · #146057 · protein
Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion (maltose bound form) in complex with the designed ar protein MBP3_16
6D67 · Maltose-binding periplasmic PROTEIN,DUAL specificity…: “Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding…”. X-ray diffraction, 2 ligands (GLC, PO4), 10 pockets (best…
- PDB
- 6D67
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,DUAL specificity protein phosphatase 1; Designed ar…
- EC
- 3.1.3.16, 3.1.3.48
- UniProt
- P0AEX9, P28562
- Ligands
- GLC, PO4
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,DUAL specificity protein phosphatase 1 (EC 3.1.3.16, 3.1.3.48) | protein | 514 | 45% helix, 20% strand | P0AEX9, P28562 |
| B | Designed ar protein MBP3_16 | protein | 128 | 57% helix, 0% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.68 | 0.84 | 28 | GLC |
| 2 | 267 | 0.65 | 0.81 | 25 | empty |
| 3 | 208 | 0.46 | 0.74 | 30 | empty |
| 4 | 72 | 0.39 | 0.78 | 16 | empty |
| 5 | 54 | 0.37 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 691 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6D67 · Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as… · the same entry in another collection · chain A against A, TM-score 1.00
- P28562 · AlphaFold monomer V2.0 prediction for dual specificity protein phosphatase 1 (P28562) · a predicted model of the same protein · chain A against A, TM-score 0.32
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 P0AEX9
- Every structure of UniProt P28562
- Elsewhere: RCSB PDB 6D67 · PDBe 6D67 · UniProt P0AEX9 · UniProt P28562
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