MolNFT v1 · #145065 · protein
Crystal structure of medicago truncatula serine hydroxymethyltransferase 3 (MTSHMT3), complexes with reaction intermediates
6CD1: “Crystal structure of medicago truncatula serine hydroxymethyltransferase 3 (MTSHMT3), complexes with reaction…”. X-ray diffraction, 3 ligands (PLS, PLG, GLY), 20 pockets (best druggability 0.87). MolNFT v1 #145065 on GenesisL1: 3D…
- PDB
- 6CD1
- Type
- protein
- Length
- 3,605 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- G7ILW0
- Ligands
- PLS, PLG, GLY
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 452 | 48% helix, 14% strand | G7ILW0 |
| B, E, F, G | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 451 | 49% helix, 14% strand | G7ILW0 |
| D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 445 | 50% helix, 15% strand | G7ILW0 |
Ligands and binding sites
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · 2 copies · chains A, B, C, D
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 2 copies · chains A, B, E, F
- GLY · Glycine · ligand · 2 copies · chains E, F, G, H
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D, E, F, G, H
- ACT · Acetate ion · additive · 3 copies · chains C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.87 | 0.89 | 114 | PLS, PLG |
| 2 | 742 | 0.81 | 0.85 | 103 | PLG |
| 3 | 429 | 0.79 | 0.88 | 62 | GLY |
| 4 | 531 | 0.77 | 0.84 | 73 | ACT |
| 5 | 423 | 0.75 | 0.84 | 50 | PLS |
Interfaces
15 interfaces between chains.
- C–D · 4075 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 4044 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 4030 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 4020 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 809 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (cofactor).
Compared structures
- 6CD1 · 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 6CD1 · PDBe 6CD1 · UniProt G7ILW0
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