Research workbench
Crystal structure of E-2-(ACETAMIDOMETHYLENE)SUCCINATE hydrolase
Analyse Crystal structure of E-2-(ACETAMIDOMETHYLENE)SUCCINATE hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KXP
- Type
- protein
- Length
- 3,216 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-(N-ACETYLAMINOMETHYLENE)SUCCINIC acid hydrolase
- UniProt
- Q988D4
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Alpha-(N-ACETYLAMINOMETHYLENE)SUCCINIC acid hydrolase | protein | 268 | 42% helix, 21% strand | Q988D4 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.83 | 0.88 | 40 | empty |
| 2 | 1062 | 0.78 | 0.80 | 87 | CL |
| 3 | 384 | 0.71 | 0.83 | 60 | empty |
| 4 | 73 | 0.71 | 0.96 | 22 | empty |
| 5 | 106 | 0.71 | 0.93 | 28 | empty |
Interfaces
14 interfaces between chains.
- A–L · 953 Ų buried · 16 hydrogen bonds · protein-protein
- H–J · 951 Ų buried · 13 hydrogen bonds · protein-protein
- I–K · 940 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 916 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 893 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3KXP · Crystal Structure of E-2-(Acetamidomethylene)succinate Hydrolase · the same entry in another collection · chain L against L, 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 Q988D4
- Elsewhere: RCSB PDB 3KXP · PDBe 3KXP · UniProt Q988D4
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