MolNFT v1 · #25891 · protein
Crystal structure of the dd-transpeptidase-carboxypeptidase from actinomadura R39
1W8Q · D-alanyl-D-alanine carboxypeptidase: “Crystal structure of the dd-transpeptidase-carboxypeptidase from actinomadura R39”. X-ray diffraction, 2 ligands (CO, SO4), 8 pockets (best druggability 0.62). MolNFT v1 #25891 on GenesisL1: 3D…
- PDB
- 1W8Q
- Type
- protein
- Length
- 1,862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- EC
- 3.4.16.4
- UniProt
- P39045
- Ligands
- CO, SO4
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 466 | 31% helix, 25% strand | P39045 |
| B, C | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 465 | 31% helix, 24% strand | P39045 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 18 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.62 | 0.78 | 46 | empty |
| 2 | 217 | 0.52 | 0.77 | 26 | empty |
| 3 | 217 | 0.51 | 0.76 | 34 | SO4 |
| 4 | 193 | 0.48 | 0.76 | 35 | SO4 |
| 5 | 286 | 0.48 | 0.72 | 40 | CO |
Interfaces
3 interfaces between chains.
- A–B · 280 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 182 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1W8Q · Crystal Structure of the DD-Transpeptidase-carboxypeptidase from Actinomadura R39 · the same entry in another collection · chain C against C, TM-score 1.00
- P39045 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase (P39045) · a predicted model of the same protein · 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 P39045
- Elsewhere: RCSB PDB 1W8Q · PDBe 1W8Q · UniProt P39045
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