Research workbench
Copper binding protein from laetisaria arvalis (LAX325)
Analyse Copper binding protein from laetisaria arvalis (LAX325) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IBI
- Type
- protein
- Length
- 607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Auxiliary activity cazyme
- Ligands
- NAG, CU
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Auxiliary activity cazyme | protein | 153 | 10% helix, 39% strand | — |
| B | Auxiliary activity cazyme | protein | 150 | 13% helix, 39% strand | — |
| C | Auxiliary activity cazyme | protein | 155 | 12% helix, 38% strand | — |
| D | Auxiliary activity cazyme | protein | 149 | 13% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, D, C, B
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 5 copies · chains A, B, C, D
- IMD · Imidazole · additive · 2 copies · chains B, C
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.65 | 0.74 | 65 | NAG |
| 2 | 139 | 0.48 | 0.78 | 30 | NAG |
| 3 | 156 | 0.48 | 0.78 | 24 | empty |
| 4 | 129 | 0.47 | 0.78 | 24 | NAG |
| 5 | 59 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 595 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 577 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 144 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 6IBI · Copper binding protein from Laetisaria arvalis (LaX325) · 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 6IBI · PDBe 6IBI
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