MolNFT v1 · #145063 · protein
Crystal structure of medicago truncatula serine hydroxymethyltransferase 3 (MTSHMT3) soaked with selenourea
6CCZ: “Crystal structure of medicago truncatula serine hydroxymethyltransferase 3 (MTSHMT3) soaked with selenourea”. X-ray diffraction, 1 ligand (SEY), 10 pockets (best druggability 0.49). MolNFT v1 #145063 on GenesisL1: 3D structure…
- PDB
- 6CCZ
- Type
- protein
- Length
- 885 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- G7ILW0
- Ligands
- SEY
- Pockets
- 10 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 443 | 50% helix, 14% strand | G7ILW0 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 442 | 49% helix, 14% strand | G7ILW0 |
Ligands and binding sites
- SEY · selenourea · ligand · 19 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.49 | 0.77 | 29 | empty |
| 2 | 186 | 0.47 | 0.75 | 23 | empty |
| 3 | 160 | 0.42 | 0.74 | 22 | empty |
| 4 | 147 | 0.42 | 0.75 | 25 | empty |
| 5 | 91 | 0.38 | 0.77 | 27 | ACT |
Interfaces
1 interface between chains.
- A–B · 685 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6CCZ · Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3)… · 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 G7ILW0
- Elsewhere: RCSB PDB 6CCZ · PDBe 6CCZ · UniProt G7ILW0
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