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The crystal structure of oxidoreductase (GFO/IDH/MOCA family) from streptococcus pneumoniae TIGR4 in complex with NADP
Analyse The crystal structure of oxidoreductase (GFO/IDH/MOCA family) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NHE
- Type
- protein
- Length
- 977 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, GFO/IDH/MOCA family
- UniProt
- Q97PV8
- Ligands
- NAP
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase, GFO/IDH/MOCA family | protein | 325 | 40% helix, 26% strand | Q97PV8 |
| B, C | Oxidoreductase, GFO/IDH/MOCA family | protein | 326 | 39% helix, 25% strand | Q97PV8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- FMT · Formic acid · additive · 13 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains B, C
- ACT · Acetate ion · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.66 | 0.77 | 71 | FMT, GOL, ACT |
| 2 | 405 | 0.61 | 0.76 | 41 | NAP, FMT |
| 3 | 428 | 0.61 | 0.76 | 40 | NAP, FMT |
| 4 | 393 | 0.59 | 0.76 | 37 | NAP, FMT |
| 5 | 94 | 0.42 | 0.78 | 22 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 1301 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 858 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4NHE · The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus… · 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 Q97PV8
- Elsewhere: RCSB PDB 4NHE · PDBe 4NHE · UniProt Q97PV8
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