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Dehydratase domain (dh) of a mycocerosic acid synthase-like (mas-like) pks, crystal form 1
Analyse Dehydratase domain (dh) of a mycocerosic acid synthase-like (mas-like) pks… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BP2
- Type
- protein
- Length
- 1,134 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycocerosic acid synthase-like polyketide synthase
- EC
- 2.3.1.-
- UniProt
- A0R1E8
- Ligands
- MG, CL
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mycocerosic acid synthase-like polyketide synthase (EC 2.3.1.-) | protein | 285 | 21% helix, 42% strand | A0R1E8 |
| B | Mycocerosic acid synthase-like polyketide synthase (EC 2.3.1.-) | protein | 284 | 22% helix, 42% strand | A0R1E8 |
| C | Mycocerosic acid synthase-like polyketide synthase (EC 2.3.1.-) | protein | 282 | 23% helix, 41% strand | A0R1E8 |
| D | Mycocerosic acid synthase-like polyketide synthase (EC 2.3.1.-) | protein | 283 | 21% helix, 42% strand | A0R1E8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D
- CL · Chloride ion · ion · 3 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, C, B, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.74 | 0.80 | 66 | EDO |
| 2 | 571 | 0.73 | 0.81 | 53 | EDO |
| 3 | 424 | 0.67 | 0.80 | 55 | empty |
| 4 | 53 | 0.66 | 0.95 | 20 | GOL |
| 5 | 109 | 0.59 | 0.86 | 22 | EDO |
Interfaces
4 interfaces between chains.
- A–D · 611 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 473 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5BP2 · Dehydratase domain (DH) of a mycocerosic acid synthase-like (MAS-like) PKS, crystal form 1 · the same entry in another collection · chain D against D, TM-score 1.00
- A0R1E8 · AlphaFold monomer V2.0 prediction for mycocerosic acid synthase-like polyketide synthase… · 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 A0R1E8
- Elsewhere: RCSB PDB 5BP2 · PDBe 5BP2 · UniProt A0R1E8
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