MolNFT v1 · #92278 · protein
Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from polaromonas sp. JS6 66
4G2N: “Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from polaromonas sp.…”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.76). MolNFT v1 #92278 on GenesisL1: 3D structure…
- PDB
- 4G2N
- Type
- protein
- Length
- 1,273 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
- UniProt
- Q120R1
- Ligands
- CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding | protein | 319 | 38% helix, 18% strand | Q120R1 |
| B | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding | protein | 318 | 39% helix, 18% strand | Q120R1 |
| D | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding | protein | 317 | 38% helix, 18% strand | Q120R1 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, D
- GOL · Glycerol · additive · 6 copies · chains A, C, B, 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 | 759 | 0.76 | 0.81 | 90 | empty |
| 2 | 617 | 0.70 | 0.78 | 59 | empty |
| 3 | 385 | 0.69 | 0.81 | 44 | empty |
| 4 | 382 | 0.65 | 0.79 | 47 | empty |
| 5 | 451 | 0.63 | 0.77 | 54 | CL |
Interfaces
5 interfaces between chains.
- A–C · 2945 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 2912 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 689 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 93 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 82 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4G2N · Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding… · the same entry in another collection · 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 Q120R1
- Elsewhere: RCSB PDB 4G2N · PDBe 4G2N · UniProt Q120R1
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