Research workbench
Crystal structure of an arginine 3RD transport system periplasmic binding protein from legionella pneumophila
Analyse Crystal structure of an arginine 3RD transport system periplasmic binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KZG
- Type
- protein
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine 3RD transport system periplasmic binding protein
- UniProt
- Q5ZV85
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Arginine 3RD transport system periplasmic binding protein | protein | 228 | 37% helix, 26% strand | Q5ZV85 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.65 | 0.77 | 57 | empty |
| 2 | 390 | 0.64 | 0.78 | 36 | empty |
| 3 | 533 | 0.61 | 0.74 | 43 | empty |
| 4 | 149 | 0.48 | 0.78 | 33 | empty |
| 5 | 94 | 0.42 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 884 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 874 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 556 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 211 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3KZG · Crystal structure of an arginine 3rd transport system periplasmic binding protein 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 Q5ZV85
- Elsewhere: RCSB PDB 3KZG · PDBe 3KZG · UniProt Q5ZV85
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