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Crystal structure of the apo form of D-ALANINE:D-alanine ligase (ddl) from streptococcus mutans
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
- 3K3P
- Type
- protein
- Length
- 635 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
- P95803
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 317 | 37% helix, 26% strand | P95803 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 318 | 37% helix, 26% strand | P95803 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.76 | 0.81 | 80 | empty |
| 2 | 725 | 0.74 | 0.79 | 74 | empty |
| 3 | 86 | 0.37 | 0.76 | 24 | empty |
| 4 | 76 | 0.37 | 0.77 | 14 | empty |
| 5 | 77 | 0.36 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1655 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3K3P · Crystal Structure of the Apo Form of D-Alanine:D-Alanine Ligase (DDl) from Streptococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- P95803 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (P95803) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P95803
- Elsewhere: RCSB PDB 3K3P · PDBe 3K3P · UniProt P95803
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