Research workbench
Crystal structure of a papain-fold protein without the catalytic cysteine from seeds of pachyrhizus erosus
Analyse Crystal structure of a papain-fold protein without the catalytic cysteine from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B1N
- Type
- protein
- Length
- 232 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPE31; Peptide (LYS)(ALA)(SER)(VAL)(GLY)
- Ligands
- NAG, FUC
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SPE31 | protein | 227 | 26% helix, 23% strand | — |
| B | Peptide (LYS)(ALA)(SER)(VAL)(GLY) | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2B1N · Crystal structure of a papain-fold protein without the catalytic cysteine from seeds of… · 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 2B1N · PDBe 2B1N
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