Research workbench
Shmt from streptococcus thermophilus TYR55SER variant in complex with PLP/D-SERINE/LYS230 gem diamine complex
Analyse Shmt from streptococcus thermophilus TYR55SER variant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TI4
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q5MCK9
- Ligands
- O3Z, MG
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 410 | 50% helix, 13% strand | Q5MCK9 |
Ligands and binding sites
- O3Z · (2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.74 | 0.84 | 50 | O3Z |
| 2 | 398 | 0.74 | 0.84 | 48 | O3Z |
| 3 | 247 | 0.68 | 0.84 | 23 | empty |
| 4 | 122 | 0.39 | 0.74 | 24 | empty |
| 5 | 125 | 0.38 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 3438 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6TI4 · SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/D-Serine/Lys230… · 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 Q5MCK9
- Elsewhere: RCSB PDB 6TI4 · PDBe 6TI4 · UniProt Q5MCK9
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