MolNFT v1 · #56033 · protein
Crystal structure of apo virginiamycin B lyase from staphylococcus aureus
2Z2O: “Crystal structure of apo virginiamycin B lyase from staphylococcus aureus”. X-ray diffraction, 1 ligand (CL), 13 pockets (best druggability 0.76). MolNFT v1 #56033 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z2O
- Type
- protein
- Length
- 1,185 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virginiamycin B lyase
- EC
- 4.2.99.-, 5.5.1.-
- UniProt
- Q53744
- Ligands
- CL
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virginiamycin B lyase (EC 4.2.99.-, 5.5.1.-) | protein | 298 | 1% helix, 51% strand | Q53744 |
| B | Virginiamycin B lyase (EC 4.2.99.-, 5.5.1.-) | protein | 293 | 1% helix, 52% strand | Q53744 |
| C | Virginiamycin B lyase (EC 4.2.99.-, 5.5.1.-) | protein | 299 | 1% helix, 52% strand | Q53744 |
| D | Virginiamycin B lyase (EC 4.2.99.-, 5.5.1.-) | protein | 295 | 1% helix, 52% strand | Q53744 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.76 | 0.79 | 91 | empty |
| 2 | 254 | 0.70 | 0.85 | 52 | empty |
| 3 | 393 | 0.69 | 0.81 | 36 | empty |
| 4 | 400 | 0.68 | 0.81 | 37 | empty |
| 5 | 359 | 0.68 | 0.81 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–D · 924 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 509 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 464 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Z2O · Crystal Structure of apo virginiamycin B lyase from Staphylococcus aureus · 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 2Z2O · PDBe 2Z2O · UniProt Q53744
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