Research workbench
Heterotetrameric sarcosine oxidase from corynebacterium sp. U-96 in complex with sulfite
Analyse Heterotetrameric sarcosine oxidase from corynebacterium sp. U-96 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ADA
- Type
- protein
- Length
- 1,646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sarcosine oxidase alpha subunit; Sarcosine oxidase beta subunit; Sarcosine oxidase gamma…
- EC
- 1.5.3.1
- UniProt
- Q50LF0, Q50LF2, Q50LE9, Q50LF1
- Ligands
- NAD, FAD, FMN, ZN, SO4, SO3
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sarcosine oxidase alpha subunit | protein | 963 | 26% helix, 30% strand | Q50LF0 |
| B | Sarcosine oxidase beta subunit (EC 1.5.3.1) | protein | 397 | 32% helix, 27% strand | Q50LF2 |
| C | Sarcosine oxidase gamma subunit | protein | 195 | 28% helix, 31% strand | Q50LE9 |
| D | Sarcosine oxidase delta subunit | protein | 91 | 16% helix, 36% strand | Q50LF1 |
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
- ZN · Zinc ion · metal · chains D
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, D
- SO3 · Sulfite ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.87 | 0.89 | 110 | NAD |
| 2 | 1176 | 0.84 | 0.85 | 138 | FAD, FMN, SO3 |
| 3 | 663 | 0.80 | 0.85 | 75 | SO4 |
| 4 | 901 | 0.80 | 0.82 | 97 | SO4 |
| 5 | 135 | 0.79 | 0.97 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3715 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 2320 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1121 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1082 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 413 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor (disulfide, flavinylation).
Compared structures
- 3ADA · Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with sulfite · the same entry in another collection · chain D against D, 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 Q50LF0
- Every structure of UniProt Q50LF2
- Every structure of UniProt Q50LE9
- Every structure of UniProt Q50LF1
- Elsewhere: RCSB PDB 3ADA · PDBe 3ADA · UniProt Q50LF0 · UniProt Q50LF2 · UniProt Q50LE9 · UniProt Q50LF1
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