MolNFT v1 · #27319 · protein
Structure of human putative dehydrogenase MGC4172 in complex with NADP
1XG5 · ARPG836: “Structure of human putative dehydrogenase MGC4172 in complex with NADP”. X-ray diffraction, 1 ligand (NAP), 8 pockets (best druggability 0.82). MolNFT v1 #27319 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XG5
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ARPG836
- UniProt
- Q6UWP2
- Ligands
- NAP
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ARPG836 | protein | 254 | 50% helix, 18% strand | Q6UWP2 |
| B | ARPG836 | protein | 244 | 48% helix, 18% strand | Q6UWP2 |
| C, D | ARPG836 | protein | 257 | 50% helix, 18% strand | Q6UWP2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.82 | 0.84 | 87 | empty |
| 2 | 475 | 0.79 | 0.86 | 58 | NAP, ACY |
| 3 | 545 | 0.78 | 0.84 | 55 | NAP, ACY |
| 4 | 358 | 0.77 | 0.87 | 44 | NAP, ACY |
| 5 | 475 | 0.66 | 0.78 | 42 | NAP |
Interfaces
4 interfaces between chains.
- B–C · 1706 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1698 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1277 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1164 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1XG5 · Structure of human putative dehydrogenase MGC4172 in complex with NADP · the same entry in another collection · chain D against D, TM-score 1.00
- Q6UWP2 · AlphaFold monomer V2.0 prediction for DEHYDROGENASE/REDUCTASE sdr family member 11… · a predicted model of the same protein · chain C 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 Q6UWP2
- Elsewhere: RCSB PDB 1XG5 · PDBe 1XG5 · UniProt Q6UWP2
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