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Crystal structure of heterotetrameric sarcosine oxidase from corynebacterium sp. U-96 in complex with folinic acid
Analyse Crystal structure of heterotetrameric sarcosine oxidase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VRQ
- Type
- protein
- Length
- 1,651 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, FON, FAD, FMN, DMG, ZN, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sarcosine oxidase alpha subunit (EC 1.5.3.1) | protein | 963 | 24% helix, 29% strand | Q50LF0 |
| B | Sarcosine oxidase beta subunit (EC 1.5.3.1) | protein | 402 | 30% helix, 27% strand | Q50LF2 |
| C | Sarcosine oxidase gamma subunit (EC 1.5.3.1) | protein | 195 | 26% helix, 30% strand | Q50LE9 |
| D | Sarcosine oxidase delta subunit (EC 1.5.3.1) | protein | 91 | 16% helix, 36% strand | Q50LF1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- FMN · Flavin mononucleotide · ligand · chains A, B
- DMG · N,N-dimethylglycine · ligand · chains B
- ZN · Zinc ion · metal · chains D
- SO4 · Sulfate ion · ion · 13 copies · chains A, C, B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.88 | 0.89 | 115 | NAD |
| 2 | 412 | 0.84 | 0.92 | 63 | FAD, DMG |
| 3 | 708 | 0.81 | 0.85 | 85 | SO4, FMN |
| 4 | 719 | 0.81 | 0.85 | 77 | SO4 |
| 5 | 163 | 0.81 | 0.96 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3724 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 2264 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 1110 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1072 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 422 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1VRQ · Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in… · 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 Q50LF0
- Every structure of UniProt Q50LF2
- Every structure of UniProt Q50LE9
- Every structure of UniProt Q50LF1
- Elsewhere: RCSB PDB 1VRQ · PDBe 1VRQ · UniProt Q50LF0 · UniProt Q50LF2 · UniProt Q50LE9 · UniProt Q50LF1
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