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Crystal structure of D-alanine--D-alanine ligase from bacillus anthracis complexed with ATP
Analyse Crystal structure of D-alanine--D-alanine ligase from bacillus anthracis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R5X
- Type
- protein
- Length
- 1,183 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
- Q81Q29
- Ligands
- ATP, CA, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 302 | 40% helix, 29% strand | Q81Q29 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 291 | 42% helix, 25% strand | Q81Q29 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 284 | 42% helix, 26% strand | Q81Q29 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 306 | 40% helix, 25% strand | Q81Q29 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 7 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains C
- EDO · 1,2-ethanediol · additive · chains D
- ACY · Acetic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.75 | 0.78 | 96 | CA, ATP |
| 2 | 1065 | 0.74 | 0.77 | 91 | ATP |
| 3 | 762 | 0.73 | 0.79 | 64 | empty |
| 4 | 595 | 0.72 | 0.80 | 53 | empty |
| 5 | 449 | 0.63 | 0.77 | 47 | CA, ATP |
Interfaces
4 interfaces between chains.
- A–B · 1196 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1147 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified (engineered).
Compared structures
- 3R5X · Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q81Q29 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q81Q29) · 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 Q81Q29
- Elsewhere: RCSB PDB 3R5X · PDBe 3R5X · UniProt Q81Q29
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