Research workbench
Crystal structure of the protein LMO2462 from listeria monocytogenes complexed with zn and phosphonate mimic of dipeptide L-leu-D-ala
Analyse Crystal structure of the protein LMO2462 from listeria monocytogenes complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NEH
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Renal dipeptidase family protein
- EC
- 4.99.1.1
- UniProt
- Q71WW4
- Ligands
- L3A, ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Renal dipeptidase family protein (EC 4.99.1.1) | protein | 309 | 41% helix, 18% strand | Q71WW4 |
Ligands and binding sites
- L3A · (2R)-3-[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]-2-methylpropanoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 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 | 400 | 0.68 | 0.81 | 39 | L3A, ZN |
| 2 | 432 | 0.62 | 0.77 | 40 | L3A, ZN |
| 3 | 52 | 0.35 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 428 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3NEH · Crystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN… · 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 Q71WW4
- Elsewhere: RCSB PDB 3NEH · PDBe 3NEH · UniProt Q71WW4
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