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The crystal structure of the heterodimer of M16B peptidase from sphingomonas sp. A1
Analyse The crystal structure of the heterodimer of M16B peptidase from sphingomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AMJ
- Type
- protein
- Length
- 1,669 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc peptidase inactive subunit; Zinc peptidase active subunit
- EC
- 3.4.24.-
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Zinc peptidase inactive subunit (EC 3.4.24.-) | protein | 414 | 47% helix, 21% strand | — |
| C, A | Zinc peptidase active subunit (EC 3.4.24.-) | protein | 422 | 46% helix, 20% strand | — |
| D | Zinc peptidase inactive subunit (EC 3.4.24.-) | protein | 411 | 46% helix, 18% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.73 | 0.78 | 68 | empty |
| 2 | 407 | 0.72 | 0.83 | 71 | empty |
| 3 | 77 | 0.72 | 0.96 | 37 | empty |
| 4 | 899 | 0.71 | 0.76 | 66 | empty |
| 5 | 549 | 0.69 | 0.79 | 66 | ZN |
Interfaces
3 interfaces between chains.
- B–A · 2612 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 1519 Ų buried · 22 hydrogen bonds · protein-protein
- C–A · 1323 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3AMJ · The crystal structure of the heterodimer of M16B peptidase from Sphingomonas sp. A1 · the same entry in another collection · chain B against B, 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 3AMJ · PDBe 3AMJ
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