MolNFT v1 · #28036 · protein
X-ray crystal structure of penicillin-binding protein- related factor a from bacillus stearothermophilus
1Y1O · Penicillin-binding protein-related factor a: “X-ray crystal structure of penicillin-binding protein- related factor a from bacillus stearothermophilus”. X-ray diffraction, 2 ligands (NI, SO4), 7 pockets (best druggability 0.60).…
- PDB
- 1Y1O
- Type
- protein
- Length
- 672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein-related factor a
- Ligands
- NI, SO4
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Penicillin-binding protein-related factor a | protein | 168 | 35% helix, 34% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.60 | 0.76 | 57 | SO4 |
| 2 | 389 | 0.57 | 0.75 | 49 | empty |
| 3 | 221 | 0.53 | 0.77 | 28 | SO4 |
| 4 | 177 | 0.50 | 0.77 | 16 | empty |
| 5 | 185 | 0.49 | 0.77 | 27 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 1492 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1466 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 640 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 264 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 251 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1Y1O · X-ray crystal Structure of Penicillin-binding protein-related factor A from Bacillus… · 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
- Elsewhere: RCSB PDB 1Y1O · PDBe 1Y1O
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