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The structure of the beta-lactamase superfamily domain of D-alanyl-D- alanine carboxypeptidase from bacillus subtilis
Analyse The structure of the beta-lactamase superfamily domain of D-alanyl-D- alanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MFD
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase dacb
- EC
- 3.4.16.4
- UniProt
- P35150
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanyl-D-alanine carboxypeptidase dacb (EC 3.4.16.4) | protein | 326 | 34% helix, 30% strand | P35150 |
| B | D-alanyl-D-alanine carboxypeptidase dacb (EC 3.4.16.4) | protein | 306 | 34% helix, 30% strand | P35150 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- CIT · Citric acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.59 | 0.75 | 49 | empty |
| 2 | 196 | 0.50 | 0.77 | 19 | empty |
| 3 | 54 | 0.30 | 0.76 | 20 | CIT |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3MFD · The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine… · the same entry in another collection · chain A against A, TM-score 1.00
- P35150 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase dacb (P35150) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P35150
- Elsewhere: RCSB PDB 3MFD · PDBe 3MFD · UniProt P35150
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