Research workbench
Crystal structure of actinomadura R39 dd-peptidase complexed with a peptidoglycan-mimetic cephalosporin
Analyse Crystal structure of actinomadura R39 dd-peptidase complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VGJ
- 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
- REC, MG, SO4
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% 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, 24% strand | P39045 |
| B, C | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 465 | 32% helix, 25% strand | P39045 |
Ligands and binding sites
- REC · Cephalosporin · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 16 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.64 | 0.73 | 76 | SO4 |
| 2 | 240 | 0.58 | 0.79 | 29 | empty |
| 3 | 236 | 0.57 | 0.79 | 33 | empty |
| 4 | 219 | 0.52 | 0.76 | 40 | REC |
| 5 | 200 | 0.49 | 0.76 | 33 | REC |
Interfaces
3 interfaces between chains.
- B–D · 344 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 341 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 114 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2VGJ · Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic… · the same entry in another collection · chain D against D, 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 2VGJ · PDBe 2VGJ · UniProt P39045
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