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Heteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution
Analyse Heteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GAG
- 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, Q3ZDQ9
- Ligands
- FOA, NAD, FAD, FMN, ZN, SO3
- Pockets
- 17 · best druggability 0.87
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, 26% strand | — |
| C | Heterotetrameric sarcosine oxidase gamma-subunit | protein | 190 | 28% helix, 31% strand | — |
| D | Heterotetrameric sarcosine oxidase delta-subunit | protein | 91 | 16% helix, 36% strand | Q3ZDQ9 |
Ligands and binding sites
- FOA · 2-furoic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- FMN · Flavin mononucleotide · ligand · chains A, B
- ZN · Zinc ion · metal · chains D
- SO3 · Sulfite ion · ion · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.87 | 0.88 | 141 | SO3, FAD, FMN, FOA |
| 2 | 1174 | 0.86 | 0.87 | 122 | NAD, GOL |
| 3 | 918 | 0.82 | 0.84 | 115 | empty |
| 4 | 802 | 0.82 | 0.85 | 98 | empty |
| 5 | 755 | 0.80 | 0.83 | 67 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3787 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 2168 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 1160 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1106 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 407 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 2GAG · Heteroteterameric 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 Q3ZDQ9
- Elsewhere: RCSB PDB 2GAG · PDBe 2GAG · UniProt Q3ZDQ8 · UniProt Q3ZDQ9
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