Research workbench
D-ALANINE:D-lactate ligase (LMDDL2) of vancomycin-resistant leuconostoc mesenteroides
Analyse D-ALANINE:D-lactate ligase (LMDDL2) of vancomycin-resistant leuconostoc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EHI
- Type
- protein
- Length
- 707 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ALANINE:D-lactate ligase
- EC
- 6.3.2.4
- UniProt
- P71454
- Ligands
- ADP, PHY, MG
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-ALANINE:D-lactate ligase (EC 6.3.2.4) | protein | 360 | 39% helix, 21% strand | P71454 |
| B | D-ALANINE:D-lactate ligase (EC 6.3.2.4) | protein | 347 | 37% helix, 22% strand | P71454 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- PHY · 1(S)-aminoethyl-(2-carboxypropyl)phosphoryl-phosphinic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.85 | 0.93 | 63 | MG, ADP, PHY |
| 2 | 731 | 0.81 | 0.85 | 71 | empty |
| 3 | 394 | 0.78 | 0.87 | 47 | empty |
| 4 | 366 | 0.65 | 0.80 | 51 | empty |
| 5 | 176 | 0.57 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2718 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1EHI · D-ALANINE:D-lactate ligase (LMDDL2) of vancomycin-resistant leuconostoc mesenteroides · 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 P71454
- Elsewhere: RCSB PDB 1EHI · PDBe 1EHI · UniProt P71454
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