Research workbench
Crystal structure of beta-aspartyl dipeptidase from thermophilic keratin degrading fervidobacterium islandicum aw-1 in complex with beta-asp-leu dipeptide
Analyse Crystal structure of beta-aspartyl dipeptidase from thermophilic keratin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CF6
- Type
- protein
- Length
- 1,497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoaspartyl dipeptidase
- EC
- 3.4.19.-
- UniProt
- A0A1B0VPV0
- Ligands
- FWO, ZN
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 372 | 29% helix, 30% strand | A0A1B0VPV0 |
| A | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 384 | 28% helix, 29% strand | A0A1B0VPV0 |
| C | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 371 | 27% helix, 27% strand | A0A1B0VPV0 |
| D | Isoaspartyl dipeptidase (EC 3.4.19.-) | protein | 370 | 26% helix, 24% strand | A0A1B0VPV0 |
Ligands and binding sites
- FWO · (2S)-2-[[(3S)-3-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-4-methyl-pentanoic acid · ligand · 4 copies · chains B, A, C, D
- ZN · Zinc ion · metal · 8 copies · chains B, A, C, D
- GOL · Glycerol · additive · 11 copies · chains B, A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.77 | 0.86 | 55 | empty |
| 2 | 357 | 0.71 | 0.83 | 43 | empty |
| 3 | 51 | 0.66 | 0.96 | 20 | empty |
| 4 | 696 | 0.65 | 0.74 | 74 | empty |
| 5 | 267 | 0.62 | 0.80 | 48 | FWO, ZN |
Interfaces
5 interfaces between chains.
- A–C · 1139 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1008 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1002 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 982 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 926 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7CF6 · Crystal structure of Beta-aspartyl dipeptidase from thermophilic keratin degrading… · 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
- Every structure of UniProt A0A1B0VPV0
- Elsewhere: RCSB PDB 7CF6 · PDBe 7CF6 · UniProt A0A1B0VPV0
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