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Crystal structure of the apo form of D-alanine: D-alanine ligase (ddl) from thermus caldophilus: a basis for the substrate-induced conformational changes
Analyse Crystal structure of the apo form of D-alanine: D-alanine ligase (ddl) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FB9
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ALANINE:D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q3T920
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-ALANINE:D-alanine ligase (EC 6.3.2.4) | protein | 322 | 30% helix, 27% strand | Q3T920 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.64 | 0.78 | 55 | empty |
| 2 | 61 | 0.38 | 0.78 | 11 | empty |
Compared structures
- 2FB9 · Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus… · 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 Q3T920
- Elsewhere: RCSB PDB 2FB9 · PDBe 2FB9 · UniProt Q3T920
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