Research workbench
Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in a cubic lattice
Analyse Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RAB
- Type
- protein
- Length
- 2,391 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multicopper oxidase
- EC
- 1.10.3.2
- UniProt
- F2NNS0
- Ligands
- CU, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H | Multicopper oxidase (EC 1.10.3.2) | protein | 299 | 13% helix, 44% strand | F2NNS0 |
| F | Multicopper oxidase (EC 1.10.3.2) | protein | 298 | 13% helix, 45% strand | F2NNS0 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 16 copies · chains A, B, G, C, H, D, E, F
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.83 | 0.92 | 35 | empty |
| 2 | 428 | 0.80 | 0.88 | 48 | empty |
| 3 | 764 | 0.77 | 0.81 | 84 | empty |
| 4 | 479 | 0.67 | 0.78 | 52 | empty |
| 5 | 421 | 0.64 | 0.78 | 52 | empty |
Interfaces
11 interfaces between chains.
- C–H · 1211 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 1211 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1211 Ų buried · 23 hydrogen bonds · protein-protein
- D–G · 1204 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 1204 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7RAB · Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in a cubic… · 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 F2NNS0
- Elsewhere: RCSB PDB 7RAB · PDBe 7RAB · UniProt F2NNS0
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