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Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in an orthorhombic 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
- 7RAC
- Type
- protein
- Length
- 3,588 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multicopper oxidase
- EC
- 1.10.3.2
- UniProt
- F2NNS0
- Ligands
- CU, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Multicopper oxidase (EC 1.10.3.2) | protein | 299 | 13% helix, 44% strand | F2NNS0 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 24 copies · chains A, B, C, D, F, E, J, K, G, H, L, I
- CA · Calcium ion · metal · 17 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 22 copies · chains A, B, D, F, C, I, L, E, H, J, G, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.83 | 0.92 | 33 | empty |
| 2 | 586 | 0.82 | 0.87 | 90 | empty |
| 3 | 367 | 0.82 | 0.91 | 41 | empty |
| 4 | 399 | 0.81 | 0.90 | 45 | empty |
| 5 | 418 | 0.80 | 0.89 | 44 | empty |
Interfaces
30 interfaces between chains.
- B–C · 1258 Ų buried · 24 hydrogen bonds · protein-protein
- F–K · 1244 Ų buried · 23 hydrogen bonds · protein-protein
- D–K · 1240 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1240 Ų buried · 27 hydrogen bonds · protein-protein
- H–L · 1237 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7RAC · Crystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in an… · 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 7RAC · PDBe 7RAC · UniProt F2NNS0
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