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The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP and D-ala-D-ala
Analyse The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C5C
- Type
- protein
- Length
- 616 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
- C4ZRI7
- Ligands
- ATP, MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 308 | 37% helix, 21% strand | C4ZRI7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 7 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.71 | 0.90 | 32 | ATP |
| 2 | 152 | 0.70 | 0.89 | 30 | ATP, MG |
| 3 | 421 | 0.58 | 0.75 | 42 | empty |
| 4 | 309 | 0.55 | 0.75 | 49 | empty |
| 5 | 240 | 0.50 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 973 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 d-amino (D-amino acid).
Compared structures
- 4C5C · The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP and… · 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 C4ZRI7
- Elsewhere: RCSB PDB 4C5C · PDBe 4C5C · UniProt C4ZRI7
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