Research workbench
D-alanine--D-alanine ligase from yersinia pestis
Analyse D-alanine--D-alanine ligase from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V4Z
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q8ZIE7
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 293 | 37% helix, 22% strand | Q8ZIE7 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 287 | 37% helix, 24% strand | Q8ZIE7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.67 | 0.77 | 52 | empty |
| 2 | 553 | 0.64 | 0.76 | 67 | empty |
| 3 | 324 | 0.59 | 0.77 | 34 | empty |
| 4 | 288 | 0.53 | 0.75 | 40 | empty |
| 5 | 159 | 0.40 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1109 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q8ZIE7
- Elsewhere: RCSB PDB 3V4Z · PDBe 3V4Z · UniProt Q8ZIE7
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