Research workbench
Crystal structure of pnpe in complex with nicotinamide adenine dinucleotide
Analyse Crystal structure of pnpe in complex with nicotinamide adenine dinucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GO4
- Type
- protein
- Length
- 3,896 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative gamma-hydroxymuconic semialdehyde dehydrogenase
- EC
- 1.2.1.3
- UniProt
- C1I208
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Putative gamma-hydroxymuconic semialdehyde dehydrogenase (EC 1.2.1.3) | protein | 487 | 41% helix, 21% strand | C1I208 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.84 | 0.85 | 70 | empty |
| 2 | 216 | 0.83 | 0.97 | 29 | empty |
| 3 | 420 | 0.83 | 0.90 | 70 | NAD |
| 4 | 209 | 0.82 | 0.96 | 29 | empty |
| 5 | 878 | 0.80 | 0.82 | 68 | NAD |
Interfaces
16 interfaces between chains.
- A–B · 3388 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 3380 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 3352 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3341 Ų buried · 47 hydrogen bonds · protein-protein
- D–E · 1130 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4GO4 · Crystal structure of PnpE in complex with Nicotinamide adenine dinucleotide · the same entry in another collection · chain E against E, 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 C1I208
- Elsewhere: RCSB PDB 4GO4 · PDBe 4GO4 · UniProt C1I208
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