MolNFT v1 · #128480 · protein
Crystal structure of burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP
5NRH · D-alanine--D-alanine ligase: “Crystal structure of burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP”. X-ray diffraction, 3 ligands (AMP, MG, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #128480 on…
- PDB
- 5NRH
- Type
- protein
- Length
- 619 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
- A3NZL3
- Ligands
- AMP, MG, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 310 | 39% helix, 22% strand | A3NZL3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 309 | 39% helix, 22% strand | A3NZL3 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.75 | 0.80 | 73 | AMP, MG |
| 2 | 303 | 0.73 | 0.86 | 58 | AMP, SO4 |
| 3 | 125 | 0.72 | 0.92 | 20 | empty |
| 4 | 327 | 0.53 | 0.74 | 35 | empty |
| 5 | 265 | 0.48 | 0.73 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1109 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5NRH · Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- A3NZL3 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (A3NZL3) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A3NZL3
- Elsewhere: RCSB PDB 5NRH · PDBe 5NRH · UniProt A3NZL3
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