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The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate
Analyse The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C5A
- Type
- protein
- Length
- 618 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase; Peptide
- EC
- 6.3.2.4
- UniProt
- C4ZRI7
- Ligands
- ADP, DS0, MG
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 306 | 38% helix, 22% strand | C4ZRI7 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 304 | 38% helix, 22% strand | C4ZRI7 |
| C | Peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- DS0 · [(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.70 | 0.95 | 27 | DS0 |
| 2 | 148 | 0.69 | 0.89 | 34 | ADP |
| 3 | 157 | 0.68 | 0.88 | 30 | ADP, MG |
| 4 | 116 | 0.63 | 0.88 | 30 | DS0 |
| 5 | 328 | 0.57 | 0.76 | 48 | empty |
Interfaces
2 interfaces between chains.
- A–B · 974 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4C5A · The X-ray crystal structures of D-alanyl-D-alanine ligase in complex 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 4C5A · PDBe 4C5A · UniProt C4ZRI7
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