Research workbench
Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp mutant Y366A in complex with acrylate
Analyse Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S00
- Type
- protein
- Length
- 1,756 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase M24
- UniProt
- D0CY07
- Ligands
- AKR, FE
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidase M24 | protein | 439 | 38% helix, 19% strand | D0CY07 |
Ligands and binding sites
- AKR · Acrylic acid · ligand · 4 copies · chains A, C, B, D
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.78 | 0.97 | 25 | empty |
| 2 | 378 | 0.78 | 0.87 | 58 | AKR, GOL |
| 3 | 121 | 0.78 | 0.96 | 23 | empty |
| 4 | 363 | 0.76 | 0.86 | 53 | GOL, AKR |
| 5 | 374 | 0.75 | 0.86 | 54 | FE, AKR, GOL |
Interfaces
3 interfaces between chains.
- A–C · 4064 Ų buried · 56 hydrogen bonds · protein-protein
- B–D · 4054 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4S00 · Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase… · 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 D0CY07
- Elsewhere: RCSB PDB 4S00 · PDBe 4S00 · UniProt D0CY07
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