MolNFT v1 · #145064 · protein
Crystal structure of medicago truncatula serine hydroxymethyltransferase 3 (MTSHMT3), plp-internal aldimine and apo form
6CD0: “Crystal structure of medicago truncatula serine hydroxymethyltransferase 3 (MTSHMT3), plp-internal aldimine…”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #145064 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6CD0
- Type
- protein
- Length
- 1,808 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- G7ILW0
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 452 | 49% helix, 14% strand | G7ILW0 |
Ligands and binding sites
- FMT · Formic acid · additive · 4 copies · chains B, C, D
- ACT · Acetate ion · additive · 3 copies · chains A, B, C, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.82 | 0.86 | 108 | ACT |
| 2 | 90 | 0.77 | 0.98 | 31 | empty |
| 3 | 118 | 0.76 | 0.96 | 28 | ACT |
| 4 | 545 | 0.76 | 0.83 | 74 | empty |
| 5 | 711 | 0.74 | 0.80 | 91 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4282 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 4256 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 781 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 764 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (cofactor, additive adduct).
Compared structures
- 6CD0 · 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 6CD0 · PDBe 6CD0 · UniProt G7ILW0
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