MolNFT v1 · #99796 · protein
Crystal structure of D-alanine-D-alanine ligase a from xanthomonas oryzae pathovar oryzae with ADP
4ME6 · D-alanine--D-alanine ligase: “Crystal structure of D-alanine-D-alanine ligase a from xanthomonas oryzae pathovar oryzae with ADP”. X-ray diffraction, 2 ligands (ADP, MG), 4 pockets (best druggability 0.50). MolNFT v1 #99796 on…
- PDB
- 4ME6
- Type
- protein
- Length
- 337 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q5H614
- Ligands
- ADP, MG
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 337 | 33% helix, 28% strand | Q5H614 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.50 | 0.74 | 41 | MG, ADP |
| 2 | 79 | 0.43 | 0.80 | 20 | empty |
| 3 | 64 | 0.35 | 0.77 | 17 | empty |
| 4 | 67 | 0.33 | 0.75 | 15 | empty |
Compared structures
- 4ME6 · Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae… · 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 Q5H614
- Elsewhere: RCSB PDB 4ME6 · PDBe 4ME6 · UniProt Q5H614
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