MolNFT v1 · #66797 · protein
The crystal structure of the D-alanyl-alanine synthetase a from salmonella enterica subsp. enterica serovar typhimurium str. LT2
3I12 · D-alanine-D-alanine ligase a: “The crystal structure of the D-alanyl-alanine synthetase a from salmonella enterica subsp. enterica serovar…”. X-ray diffraction, 1 ligand (ADP), 11 pockets (best druggability 0.83). MolNFT v1 #66797…
- PDB
- 3I12
- Type
- protein
- Length
- 1,409 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine-D-alanine ligase a
- EC
- 6.3.2.4
- UniProt
- P0A1F0
- Ligands
- ADP
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine-D-alanine ligase a (EC 6.3.2.4) | protein | 360 | 32% helix, 26% strand | P0A1F0 |
| B | D-alanine-D-alanine ligase a (EC 6.3.2.4) | protein | 346 | 30% helix, 27% strand | P0A1F0 |
| C | D-alanine-D-alanine ligase a (EC 6.3.2.4) | protein | 348 | 31% helix, 26% strand | P0A1F0 |
| D | D-alanine-D-alanine ligase a (EC 6.3.2.4) | protein | 355 | 32% helix, 26% strand | P0A1F0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.83 | 0.85 | 109 | ADP |
| 2 | 1026 | 0.81 | 0.82 | 82 | empty |
| 3 | 1059 | 0.81 | 0.82 | 83 | empty |
| 4 | 863 | 0.81 | 0.83 | 64 | empty |
| 5 | 566 | 0.78 | 0.84 | 60 | ADP |
Interfaces
4 interfaces between chains.
- A–B · 2350 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2283 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 652 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 83 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3I12 · The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A1F0 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase a (P0A1F0) · 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 P0A1F0
- Elsewhere: RCSB PDB 3I12 · PDBe 3I12 · UniProt P0A1F0
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