Research workbench
Dickeya chrysanthemi complex with L-asp at pH 5.6
Analyse Dickeya chrysanthemi complex with L-asp at pH 5.6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PAE
- Type
- protein
- Length
- 1,248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P06608
- Ligands
- ASP
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase (EC 3.5.1.1) | protein | 317 | 32% helix, 24% strand | P06608 |
| B | L-asparaginase (EC 3.5.1.1) | protein | 308 | 33% helix, 24% strand | P06608 |
| C | L-asparaginase (EC 3.5.1.1) | protein | 313 | 33% helix, 24% strand | P06608 |
| D | L-asparaginase (EC 3.5.1.1) | protein | 310 | 34% helix, 24% strand | P06608 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.80 | 0.94 | 40 | empty |
| 2 | 107 | 0.73 | 0.95 | 44 | empty |
| 3 | 80 | 0.70 | 0.95 | 29 | empty |
| 4 | 509 | 0.67 | 0.78 | 49 | ASP |
| 5 | 484 | 0.63 | 0.76 | 47 | ASP |
Interfaces
6 interfaces between chains.
- A–C · 2244 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2211 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 1128 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1123 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 891 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 P06608
- Elsewhere: RCSB PDB 6PAE · PDBe 6PAE · UniProt P06608
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