MolNFT v1 · #114439 · protein
Crystal structure of AMP complexed D-alanine-D-alanine LIGASE(DDL) from yersinia pestis
5BPH · D-alanine--D-alanine ligase: “Crystal structure of AMP complexed D-alanine-D-alanine LIGASE(DDL) from yersinia pestis”. X-ray diffraction, 2 ligands (AMP, NA), 11 pockets (best druggability 0.88). MolNFT v1 #114439 on GenesisL1: 3D…
- PDB
- 5BPH
- Type
- protein
- Length
- 1,220 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
- AMP, NA
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 306 | 38% helix, 23% strand | Q8ZIE7 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 305 | 38% helix, 21% strand | Q8ZIE7 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 303 | 36% helix, 22% strand | Q8ZIE7 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 6 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.88 | 0.90 | 126 | AMP, ACT |
| 2 | 230 | 0.80 | 0.93 | 39 | AMP |
| 3 | 745 | 0.72 | 0.78 | 81 | GOL, ACT |
| 4 | 188 | 0.71 | 0.88 | 30 | AMP |
| 5 | 309 | 0.62 | 0.79 | 41 | ACT |
Interfaces
4 interfaces between chains.
- A–D · 1072 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 619 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 550 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 513 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- Q8ZIE7 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q8ZIE7) · a predicted model of the same protein · chain A 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 5BPH · PDBe 5BPH · UniProt Q8ZIE7
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