Research workbench
Crystal structure of E. COLI NADP dependent enzyme
Analyse Crystal structure of E. COLI NADP dependent enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JZ4
- Type
- protein
- Length
- 1,924 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate-semialdehyde dehydrogenase [NADP+]
- EC
- 1.2.1.16
- UniProt
- P25526
- Ligands
- NAP
- Pockets
- 17 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.16) | protein | 481 | 42% helix, 23% strand | P25526 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.89 | 0.91 | 90 | empty |
| 2 | 1010 | 0.86 | 0.87 | 107 | empty |
| 3 | 1088 | 0.85 | 0.86 | 107 | empty |
| 4 | 389 | 0.84 | 0.93 | 46 | empty |
| 5 | 359 | 0.63 | 0.79 | 52 | NAP |
Interfaces
6 interfaces between chains.
- A–B · 2580 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2557 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1003 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 984 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 859 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3JZ4 · Crystal structure of E. coli NADP dependent enzyme · the same entry in another collection · chain D against D, TM-score 1.00
- P25526 · AlphaFold monomer V2.0 prediction for succinate-semialdehyde dehydrogenase [NADP(+)] gabd… · a predicted model of the same protein · 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 P25526
- Elsewhere: RCSB PDB 3JZ4 · PDBe 3JZ4 · UniProt P25526
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