MolNFT v1 · #117654 · protein
Crystal structure of dapb in complex with NADP+ from corynebacterium glutamicum
5EES · 4-hydroxy-tetrahydrodipicolinate reductase: “Crystal structure of dapb in complex with NADP+ from corynebacterium glutamicum”. X-ray diffraction, 2 ligands (NAP, SO4), 2 pockets (best druggability 0.51). MolNFT v1 #117654 on…
- PDB
- 5EES
- Type
- protein
- Length
- 247 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate reductase
- EC
- 1.17.1.8
- UniProt
- P40110
- Ligands
- NAP, SO4
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 247 | 36% helix, 26% strand | P40110 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.51 | 0.75 | 33 | SO4 |
| 2 | 57 | 0.28 | 0.74 | 14 | empty |
Compared structures
- 5EES · Crystal structure of DapB in complex with NADP+ from Corynebacterium glutamicum · the same entry in another collection · chain A against A, TM-score 1.00
- P40110 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (P40110) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P40110
- Elsewhere: RCSB PDB 5EES · PDBe 5EES · UniProt P40110
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