Research workbench
Crystal structure of apo D-ALANINE:D-alanine ligase (ddl) from mycobacterium tuberculosis
Analyse Crystal structure of apo D-ALANINE:D-alanine ligase (ddl) from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LWB
- Type
- protein
- Length
- 621 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
- P95114
- Ligands
- NO3
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 323 | 33% helix, 28% strand | P95114 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 298 | 34% helix, 26% strand | P95114 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.79 | 0.88 | 60 | NO3 |
| 2 | 241 | 0.69 | 0.85 | 50 | NO3 |
| 3 | 200 | 0.60 | 0.82 | 40 | empty |
| 4 | 115 | 0.50 | 0.81 | 21 | empty |
| 5 | 238 | 0.48 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 891 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3LWB · Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from Mycobacterium tuberculosis · 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 P95114
- Elsewhere: RCSB PDB 3LWB · PDBe 3LWB · UniProt P95114
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