MolNFT v1 · #184081 · protein
Mannitol-1-phosphate bound to the phosphatase domain of the bifunctional mannitol-1-phosphate DEHYDROGENASE/PHOSPHATASE mtld-D16A from acinetobacter baumannii
7OCS · Had hydrolase, family ia, variant 3: “Mannitol-1-phosphate bound to the phosphatase domain of the bifunctional mannitol-1-phosphate…”. X-ray diffraction, 5 ligands (44H, NA, MG), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 7OCS
- Type
- protein
- Length
- 2,622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Had hydrolase, family ia, variant 3
- UniProt
- D0C7J2
- Ligands
- 44H, NA, MG, SO4, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Had hydrolase, family ia, variant 3 | protein | 682 | 56% helix, 14% strand | D0C7J2 |
| B | Had hydrolase, family ia, variant 3 | protein | 683 | 55% helix, 14% strand | D0C7J2 |
| C | Had hydrolase, family ia, variant 3 | protein | 572 | 52% helix, 17% strand | D0C7J2 |
| D | Had hydrolase, family ia, variant 3 | protein | 685 | 56% helix, 14% strand | D0C7J2 |
Ligands and binding sites
- 44H · D-Mannitol-1-phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains B, C
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D, B, C
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, C
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.87 | 0.90 | 107 | EDO, PGE |
| 2 | 525 | 0.84 | 0.90 | 72 | empty |
| 3 | 1014 | 0.80 | 0.82 | 92 | NA |
| 4 | 1042 | 0.79 | 0.81 | 87 | GOL, EDO |
| 5 | 235 | 0.75 | 0.90 | 41 | PG4 |
Interfaces
5 interfaces between chains.
- A–D · 4264 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 4165 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1223 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 375 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7OCS · Mannitol-1-phosphate bound to the phosphatase domain of the bifunctional… · 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 D0C7J2
- Elsewhere: RCSB PDB 7OCS · PDBe 7OCS · UniProt D0C7J2
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