Research workbench
Oligo-peptide binding protein (oppa) complexed with kdk
Analyse Oligo-peptide binding protein (oppa) complexed with kdk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B4Z
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (oligo-peptide binding protein); Protein (peptide lys-asp-lys)
- UniProt
- P06202
- Ligands
- IUM
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (oligo-peptide binding protein) | protein | 517 | 34% helix, 22% strand | P06202 |
| B | Protein (peptide lys-asp-lys) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- IUM · Uranyl (VI) ion · metal · 8 copies · chains A
- ACT · Acetate ion · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.53 | 0.88 | 23 | empty |
| 2 | 51 | 0.39 | 0.81 | 15 | empty |
| 3 | 92 | 0.38 | 0.77 | 22 | empty |
| 4 | 79 | 0.35 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 500 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1B4Z · Oligo-peptide binding protein (oppa) complexed with kdk · the same entry in another collection · chain A against A, TM-score 1.00
- P06202 · AlphaFold monomer V2.0 prediction for periplasmic oligopeptide- binding protein (P06202) · a predicted model of the same protein · 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 P06202
- Elsewhere: RCSB PDB 1B4Z · PDBe 1B4Z · UniProt P06202
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