MolNFT v1 · #188674 · protein
Crystal structure of D-alanine--D-alanine ligase from klebsiella pneumoniae subsp. pneumoniae in complex with AMP
7U56: “Crystal structure of D-alanine--D-alanine ligase from klebsiella pneumoniae subsp. pneumoniae in complex with…”. X-ray diffraction, 3 ligands (AMP, MG, CL), 2 pockets (best druggability 0.83). MolNFT v1 #188674 on GenesisL1: 3D…
- PDB
- 7U56
- Type
- protein
- Length
- 686 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
- A0A0H3GSI5
- Ligands
- AMP, MG, CL
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 346 | 31% helix, 28% strand | A0A0H3GSI5 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 340 | 32% helix, 27% strand | A0A0H3GSI5 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.83 | 0.84 | 116 | EDO, AMP, MG, CL |
| 2 | 1143 | 0.82 | 0.83 | 104 | AMP, MG, EDO, CL |
Interfaces
1 interface between chains.
- A–B · 2273 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7U56 · Crystal Structure of D-alanine--D-alanine ligase from Klebsiella pneumoniae subsp.… · 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 A0A0H3GSI5
- Elsewhere: RCSB PDB 7U56 · PDBe 7U56 · UniProt A0A0H3GSI5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.