MolNFT v1 · #112547 · protein
Crystal structure of glyceraldehyde oxidoreductase
4ZOH · Putative oxidoreductase molybdopterin-binding subunit: “Crystal structure of glyceraldehyde oxidoreductase”. X-ray diffraction, 4 ligands (FES, MCN, FAD), 10 pockets (best druggability 0.80). MolNFT v1 #112547 on GenesisL1: 3D…
- PDB
- 4ZOH
- Type
- protein
- Length
- 1,136 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase molybdopterin-binding subunit; Putative oxidoreductase…
- UniProt
- Q96Y29, Q974U9, Q974V0
- Ligands
- FES, MCN, FAD, MO
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative oxidoreductase molybdopterin-binding subunit | protein | 701 | 31% helix, 26% strand | Q96Y29 |
| B | Putative oxidoreductase FAD-binding subunit | protein | 274 | 35% helix, 28% strand | Q974U9 |
| C | Putative oxidoreductase iron-sulfur subunit | protein | 161 | 37% helix, 20% strand | Q974V0 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, A
- MCN · Pterin cytosine dinucleotide · ligand · chains A, C
- FAD · Flavin-adenine dinucleotide · ligand · chains B, C
- MO · Molybdenum atom · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.80 | 0.86 | 67 | FAD |
| 2 | 447 | 0.78 | 0.86 | 59 | MCN, MO, 1PE |
| 3 | 63 | 0.72 | 0.98 | 25 | empty |
| 4 | 452 | 0.67 | 0.79 | 54 | PEG |
| 5 | 389 | 0.61 | 0.77 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2288 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1712 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1023 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4ZOH · Crystal structure of glyceraldehyde oxidoreductase · 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 Q96Y29
- Every structure of UniProt Q974U9
- Every structure of UniProt Q974V0
- Elsewhere: RCSB PDB 4ZOH · PDBe 4ZOH · UniProt Q96Y29 · UniProt Q974U9 · UniProt Q974V0
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