MolNFT v1 · #37721 · protein
Heterotetrameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution
2GAH · Heterotetrameric sarcosine oxidase alpha-subunit: “Heterotetrameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution”. X-ray diffraction, 5 ligands (NAD, FAD, FMN), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 2GAH
- Type
- protein
- Length
- 1,649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heterotetrameric sarcosine oxidase alpha-subunit; Heterotetrameric sarcosine oxidase…
- UniProt
- Q3ZDQ8, Q3ZDR0, Q3ZDQ7, Q3ZDQ9
- Ligands
- NAD, FAD, FMN, FOA, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heterotetrameric sarcosine oxidase alpha-subunit | protein | 965 | 24% helix, 30% strand | Q3ZDQ8 |
| B | Heterotetrameric sarcosine oxidase beta-subunit | protein | 403 | 31% helix, 27% strand | Q3ZDR0 |
| C | Heterotetrameric sarcosine oxidase gamma-subunit | protein | 190 | 27% helix, 31% strand | Q3ZDQ7 |
| D | Heterotetrameric sarcosine oxidase delta-subunit | protein | 91 | 16% helix, 36% strand | Q3ZDQ9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- FMN · Flavin mononucleotide · ligand · chains A, B
- FOA · 2-furoic acid · ligand · chains B
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.86 | 0.87 | 127 | NAD |
| 2 | 411 | 0.83 | 0.91 | 60 | FAD, FOA |
| 3 | 784 | 0.82 | 0.85 | 90 | empty |
| 4 | 753 | 0.82 | 0.85 | 102 | FMN |
| 5 | 910 | 0.80 | 0.82 | 89 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3739 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 2182 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 1135 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1096 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 407 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified, 1 cofactor (engineered, flavinylation).
Compared structures
- 2GAH · Heterotetrameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution · 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 Q3ZDQ8
- Every structure of UniProt Q3ZDR0
- Every structure of UniProt Q3ZDQ7
- Every structure of UniProt Q3ZDQ9
- Elsewhere: RCSB PDB 2GAH · PDBe 2GAH · UniProt Q3ZDQ8 · UniProt Q3ZDR0 · UniProt Q3ZDQ7 · UniProt Q3ZDQ9
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