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Crystal structure of catalytically inactive H270A virginiamycin B lyase from staphylococcus aureus with quinupristin
Analyse Crystal structure of catalytically inactive H270A virginiamycin B lyase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z2P
- Type
- protein
- Length
- 600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virginiamycin B lyase; Quinupristin
- EC
- 4.2.99.-, 5.5.1.-
- UniProt
- Q53744
- Ligands
- DOL, MHT, MG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Virginiamycin B lyase (EC 4.2.99.-, 5.5.1.-) | protein | 293 | 1% helix, 51% strand | Q53744 |
| C, D | Quinupristin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- DOL · 5-(2-diethylamino-ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone · ligand · 2 copies · chains A, C, B, D
- MHT · (3R)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.75 | 0.78 | 76 | MHT |
| 2 | 390 | 0.67 | 0.80 | 36 | empty |
| 3 | 347 | 0.58 | 0.76 | 48 | DOL |
Interfaces
4 interfaces between chains.
- A–C · 497 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 493 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 343 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 2Z2P · Crystal Structure of catalytically inactive H270A virginiamycin B lyase from… · the same entry in another collection · 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 Q53744
- Elsewhere: RCSB PDB 2Z2P · PDBe 2Z2P · UniProt Q53744
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