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Crystal structure of D-alanine-D-alnine ligase from xanthomonas oryzae pv. oryzae with ATP
Analyse Crystal structure of D-alanine-D-alnine ligase from xanthomonas oryzae pv.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R5F
- Type
- protein
- Length
- 343 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase 1
- EC
- 6.3.2.4
- UniProt
- Q2P8P8
- Ligands
- ATP, MG
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase 1 (EC 6.3.2.4) | protein | 343 | 34% helix, 27% strand | Q2P8P8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.56 | 0.76 | 40 | ATP, MG |
| 2 | 73 | 0.43 | 0.81 | 21 | empty |
| 3 | 62 | 0.35 | 0.77 | 14 | empty |
Compared structures
- 3R5F · Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP · 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 Q2P8P8
- Elsewhere: RCSB PDB 3R5F · PDBe 3R5F · UniProt Q2P8P8
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