Research workbench
Structure of a meso-diaminopimelate dehydrogenase in complex with NADP
Analyse Structure of a meso-diaminopimelate dehydrogenase in complex with NADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WYC
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meso-diaminopimelate D-dehydrogenase
- EC
- 1.4.1.16
- UniProt
- G1UII1
- Ligands
- NES, NAP
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16) | protein | 327 | 40% helix, 27% strand | G1UII1 |
Ligands and binding sites
- NES · 2-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-ethanesulfonic acid · ligand · 4 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.69 | 0.77 | 50 | NAP, NES |
| 2 | 634 | 0.68 | 0.77 | 53 | NAP, NES |
| 3 | 178 | 0.45 | 0.75 | 37 | empty |
| 4 | 81 | 0.33 | 0.74 | 19 | empty |
| 5 | 68 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3314 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 3WYC · Structure of a meso-diaminopimelate dehydrogenase in complex with NADP · the same entry in another collection · chain A against A, TM-score 1.00
- G1UII1 · AlphaFold monomer V2.0 prediction for meso-diaminopimelate D-dehydrogenase (G1UII1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 G1UII1
- Elsewhere: RCSB PDB 3WYC · PDBe 3WYC · UniProt G1UII1
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