MolNFT v1 · #165606 · protein
Crystal structure of a peptidoglycan release complex, sagb-spdc, in lipidic cubic phase
6U0O · Lysostaphin resistance protein a: “Crystal structure of a peptidoglycan release complex, sagb-spdc, in lipidic cubic phase”. X-ray diffraction, 2 ligands (AE3, SO4), 7 pockets (best druggability 0.76). MolNFT v1 #165606 on…
- PDB
- 6U0O
- Type
- protein
- Length
- 541 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysostaphin resistance protein a; LYZ2 domain-containing protein; Flag peptide
- UniProt
- Q2YYX7, Q2FXF4
- Ligands
- AE3, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysostaphin resistance protein a | protein | 248 | 73% helix, 1% strand | Q2YYX7 |
| B | LYZ2 domain-containing protein | protein | 288 | 52% helix, 9% strand | Q2FXF4 |
| D | Flag peptide | protein | 5 | 0% helix, 60% strand | — |
Ligands and binding sites
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · 2 copies · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- FLC · Citrate anion · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.76 | 0.81 | 40 | FLC, PG4 |
| 2 | 50 | 0.46 | 0.85 | 13 | empty |
| 3 | 51 | 0.46 | 0.85 | 11 | empty |
| 4 | 112 | 0.45 | 0.77 | 19 | AE3 |
| 5 | 100 | 0.40 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1123 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 359 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6U0O · Crystal structure of a peptidoglycan release complex, SagB-SpdC, in lipidic cubic phase · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YYX7 · AlphaFold monomer V2.0 prediction for lysostaphin resistance protein a (Q2YYX7) · a predicted model of the same protein · 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 Q2YYX7
- Every structure of UniProt Q2FXF4
- Elsewhere: RCSB PDB 6U0O · PDBe 6U0O · UniProt Q2YYX7 · UniProt Q2FXF4
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