Research workbench
X-ray crystal structure of a periplasmic oligopeptide-binding PROTEIN/OLIGOPEPTIDE ABC TRANSPORTER(OPPAIV) from borrelia burgdorferi
Analyse X-ray crystal structure of a periplasmic oligopeptide-binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GL8
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptide ABC transporter oppaiv; Peptide of unknown sequence
- UniProt
- H7C7K8
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oligopeptide ABC transporter oppaiv | protein | 500 | 36% helix, 23% strand | H7C7K8 |
| C, D | Peptide of unknown sequence | protein | 4 | 0% helix, 25% strand | — |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.86 | 0.94 | 75 | empty |
| 2 | 224 | 0.82 | 0.95 | 41 | empty |
| 3 | 179 | 0.79 | 0.95 | 35 | empty |
| 4 | 168 | 0.61 | 0.83 | 31 | empty |
| 5 | 147 | 0.58 | 0.83 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 408 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 387 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 192 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GL8 · X-ray crystal structure of a periplasmic oligopeptide-binding protein/Oligopeptide ABC… · 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 H7C7K8
- Elsewhere: RCSB PDB 4GL8 · PDBe 4GL8 · UniProt H7C7K8
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