MolNFT v1 · #77516 · protein
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase gapn from methanocaldococcus jannaschii dsm 2661 complexed with NADP
3RHD · Lactaldehyde dehydrogenase: “Crystal structure of glyceraldehyde-3-phosphate dehydrogenase gapn from methanocaldococcus jannaschii dsm…”. X-ray diffraction, 1 ligand (NAP), 20 pockets (best druggability 0.89). MolNFT v1 #77516 on…
- PDB
- 3RHD
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactaldehyde dehydrogenase
- EC
- 1.2.1.22
- UniProt
- Q58806
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lactaldehyde dehydrogenase (EC 1.2.1.22) | protein | 456 | 44% helix, 22% strand | Q58806 |
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
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.89 | 0.90 | 134 | empty |
| 2 | 482 | 0.86 | 0.93 | 81 | empty |
| 3 | 264 | 0.82 | 0.93 | 48 | empty |
| 4 | 1178 | 0.77 | 0.79 | 113 | empty |
| 5 | 1111 | 0.76 | 0.78 | 112 | NAP |
Interfaces
6 interfaces between chains.
- A–B · 2298 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2285 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1079 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1062 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 788 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3RHD · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58806 · AlphaFold monomer V2.0 prediction for lactaldehyde dehydrogenase (Q58806) · 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 Q58806
- Elsewhere: RCSB PDB 3RHD · PDBe 3RHD · UniProt Q58806
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