MolNFT v1 · #70998 · protein
Crystal structure of the LYS265ARG peg-crystallized mutant of monomeric sarcosine oxidase
3M13: “Crystal structure of the LYS265ARG peg-crystallized mutant of monomeric sarcosine oxidase”. X-ray diffraction, 3 ligands (FAD, CL, PO4), 13 pockets (best druggability 0.83). MolNFT v1 #70998 on GenesisL1: 3D structure, binding sites…
- PDB
- 3M13
- Type
- protein
- Length
- 1,524 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monomeric sarcosine oxidase
- EC
- 1.5.3.1
- UniProt
- P40859
- Ligands
- FAD, CL, PO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 381 | 31% helix, 30% strand | P40859 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.83 | 0.91 | 69 | FAD, CL |
| 2 | 431 | 0.83 | 0.91 | 64 | FAD, CL |
| 3 | 424 | 0.83 | 0.91 | 70 | FAD, CL |
| 4 | 427 | 0.83 | 0.91 | 66 | FAD, CL |
| 5 | 117 | 0.42 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–D · 985 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 985 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 353 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 3M13 · Crystal Structure of the Lys265Arg PEG-crystallized mutant of monomeric sarcosine oxidase · the same entry in another collection · chain A against A, TM-score 1.00
- P40859 · AlphaFold monomer V2.0 prediction for monomeric sarcosine oxidase (P40859) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P40859
- Elsewhere: RCSB PDB 3M13 · PDBe 3M13 · UniProt P40859
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