Research workbench
Crystal structure of ADP and D-alanyl-D-alanine complexed D-alanine-D- alanine LIGASE(DDL) from yersinia pestis
Analyse Crystal structure of ADP and D-alanyl-D-alanine complexed D-alanine-D- alanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C1P
- Type
- protein
- Length
- 1,197 residues
- Chains
- 4
- 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
- Ligands
- ADP, NA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 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 | 289 | 38% helix, 22% strand | Q8ZIE7 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 298 | 36% helix, 22% strand | Q8ZIE7 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 306 | 38% helix, 22% strand | Q8ZIE7 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 304 | 38% helix, 23% strand | Q8ZIE7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.79 | 0.81 | 86 | GOL, ADP |
| 2 | 1055 | 0.77 | 0.79 | 101 | GOL, ADP |
| 3 | 209 | 0.73 | 0.88 | 33 | ADP |
| 4 | 595 | 0.70 | 0.79 | 77 | ACT |
| 5 | 708 | 0.66 | 0.75 | 68 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1098 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1068 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 605 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 d-amino (D-amino acid).
Compared structures
- 5C1P · Crystal structure of ADP and D-alanyl-D-alanine complexed D-alanine-D-alanine ligase(DDL)… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8ZIE7 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q8ZIE7) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 5C1P · PDBe 5C1P · UniProt Q8ZIE7
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