MolNFT v1 · #21179 · protein
A novel NAD binding protein revealed by the crystal structure of E. COLI 2,3-diketogulonate reductase (yiak) northeast structural genomics consortium target ER82
1S20 · Hypothetical oxidoreductase yiak: “A novel NAD binding protein revealed by the crystal structure of E. COLI 2,3-diketogulonate reductase (yiak)…”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 1S20
- Type
- protein
- Length
- 2,672 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical oxidoreductase yiak
- EC
- 1.1.1.-
- UniProt
- P37672
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, H | Hypothetical oxidoreductase yiak (EC 1.1.1.-) | protein | 334 | 44% helix, 18% strand | P37672 |
| F | Hypothetical oxidoreductase yiak (EC 1.1.1.-) | protein | 333 | 43% helix, 17% strand | P37672 |
| G | Hypothetical oxidoreductase yiak (EC 1.1.1.-) | protein | 335 | 44% helix, 18% strand | P37672 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F, G, H
- TLA · L(+)-tartaric acid · additive · 6 copies · chains A, B, D, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.80 | 0.99 | 22 | empty |
| 2 | 86 | 0.79 | 0.98 | 22 | empty |
| 3 | 80 | 0.78 | 0.98 | 22 | empty |
| 4 | 75 | 0.78 | 0.98 | 20 | empty |
| 5 | 806 | 0.77 | 0.80 | 90 | empty |
Interfaces
10 interfaces between chains.
- E–F · 3795 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 3793 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 3791 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 3778 Ų buried · 37 hydrogen bonds · protein-protein
- A–G · 536 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 120 modified (engineered).
Compared structures
- 1S20 · A novel NAD binding protein revealed by the crystal structure of E. Coli… · the same entry in another collection · chain H against H, TM-score 1.00
- P37672 · AlphaFold monomer V2.0 prediction for 2,3-diketo-L-gulonate reductase (P37672) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P37672
- Elsewhere: RCSB PDB 1S20 · PDBe 1S20 · UniProt P37672
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