MolNFT v1 · #114437 · protein
Crystal structure of ADP complexed D-alanine-D-alanine LIGASE(DDL) from yersinia pestis
5BPF: “Crystal structure of ADP complexed D-alanine-D-alanine LIGASE(DDL) from yersinia pestis”. X-ray diffraction, 2 ligands (ADP, NA), 10 pockets (best druggability 0.80). MolNFT v1 #114437 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5BPF
- Type
- protein
- Length
- 1,194 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine-D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q8ZIE7
- Ligands
- ADP, NA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine-D-alanine ligase (EC 6.3.2.4) | protein | 291 | 37% helix, 24% strand | Q8ZIE7 |
| B | D-alanine-D-alanine ligase (EC 6.3.2.4) | protein | 301 | 34% helix, 22% strand | Q8ZIE7 |
| C | D-alanine-D-alanine ligase (EC 6.3.2.4) | protein | 306 | 37% helix, 23% strand | Q8ZIE7 |
| D | D-alanine-D-alanine ligase (EC 6.3.2.4) | protein | 296 | 38% helix, 23% strand | Q8ZIE7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, C, D
- ACT · Acetate ion · additive · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.80 | 0.81 | 114 | GOL, ADP, ACT |
| 2 | 1093 | 0.74 | 0.77 | 115 | GOL, ADP |
| 3 | 191 | 0.72 | 0.89 | 33 | ADP |
| 4 | 601 | 0.70 | 0.79 | 82 | ACT, GOL |
| 5 | 854 | 0.70 | 0.75 | 87 | GOL, ACT |
Interfaces
3 interfaces between chains.
- A–B · 1105 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1089 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5BPF · Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis · the same entry in another collection · chain C against C, TM-score 1.00
- Q8ZIE7 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q8ZIE7) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q8ZIE7
- Elsewhere: RCSB PDB 5BPF · PDBe 5BPF · UniProt Q8ZIE7
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