Research workbench
Crystal structure of a complex between actinomadura R39 dd- peptidase and a boronate inhibitor
Analyse Crystal structure of a complex between actinomadura R39 dd- peptidase and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XK1
- 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
- EWB, CO, SO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 30% 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 | 30% helix, 23% strand | P39045 |
| B, C | D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4) | protein | 465 | 30% helix, 25% strand | P39045 |
Ligands and binding sites
- EWB · [(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-) · ligand · 4 copies · chains A, C, B, D
- CO · Cobalt (II) ion · metal · 4 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.81 | 0.82 | 99 | EWB, SO4 |
| 2 | 618 | 0.75 | 0.81 | 49 | empty |
| 3 | 432 | 0.72 | 0.82 | 53 | EWB, SO4 |
| 4 | 795 | 0.70 | 0.77 | 99 | EWB |
| 5 | 213 | 0.52 | 0.77 | 35 | EWB |
Interfaces
5 interfaces between chains.
- B–C · 680 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 556 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 322 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2XK1 · Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate… · 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 B 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 2XK1 · PDBe 2XK1 · UniProt P39045
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