MolNFT v1 · #106467 · protein
Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp in complex with mes
4RZY · Peptidase M24: “Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp in complex with mes”. X-ray diffraction, 1 ligand (FE), 17 pockets (best druggability 0.80). MolNFT v1 #106467 on GenesisL1…
- PDB
- 4RZY
- 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
- FE
- Pockets
- 17 · best druggability 0.80
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
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.80 | 0.92 | 60 | empty |
| 2 | 134 | 0.79 | 0.97 | 29 | empty |
| 3 | 357 | 0.75 | 0.86 | 54 | MES |
| 4 | 369 | 0.75 | 0.85 | 61 | MES |
| 5 | 376 | 0.74 | 0.85 | 64 | MES |
Interfaces
3 interfaces between chains.
- B–D · 4054 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 4041 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 334 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RZY · 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 4RZY · PDBe 4RZY · UniProt D0CY07
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