Research workbench
Psabc from streptococcus pneumoniae in complex with Fab
Analyse Psabc from streptococcus pneumoniae in complex with Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KYO
- Type
- protein
- Length
- 925 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manganese ABC transporter, ATP-binding protein; Fab heavy chain; Fab light chain…
- UniProt
- A0A0H2ZNF3, A0A0H2ZPI2
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Manganese ABC transporter, ATP-binding protein | protein | 234 | 38% helix, 24% strand | A0A0H2ZNF3 |
| H | Fab heavy chain | protein | 217 | 4% helix, 49% strand | — |
| L | Fab light chain | protein | 216 | 6% helix, 52% strand | — |
| C | Manganese ABC transporter, permease protein | protein | 258 | 83% helix, 0% strand | A0A0H2ZPI2 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.64 | 0.76 | 56 | empty |
| 2 | 175 | 0.62 | 0.83 | 20 | empty |
| 3 | 224 | 0.55 | 0.77 | 22 | empty |
| 4 | 221 | 0.49 | 0.75 | 34 | empty |
| 5 | 127 | 0.46 | 0.78 | 22 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1978 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1210 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 804 Ų buried · 14 hydrogen bonds · protein-protein
- B–L · 389 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7KYO · PsaBC from Streptococcus pneumoniae in complex with Fab · the same entry in another collection · chain B against B, 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 A0A0H2ZNF3
- Every structure of UniProt A0A0H2ZPI2
- Elsewhere: RCSB PDB 7KYO · PDBe 7KYO · UniProt A0A0H2ZNF3 · UniProt A0A0H2ZPI2
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