Research workbench
Shmt from streptococcus thermophilus TYR55THR variant in complex with D-serine both as external aldimine and as non-covalent complex
Analyse Shmt from streptococcus thermophilus TYR55THR variant in complex with D-serine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TGH
- Type
- protein
- Length
- 1,640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q5MCK9
- Ligands
- EVM, DSN, PLP, NA
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 410 | 47% helix, 13% strand | Q5MCK9 |
Ligands and binding sites
- EVM · L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene] · ligand · 2 copies · chains A, C, B, D
- DSN · D-serine · ligand · 2 copies · chains A, C, B, D
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, C, B, D
- NA · Sodium ion · metal · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.83 | 0.84 | 109 | empty |
| 2 | 445 | 0.77 | 0.85 | 51 | DSN, PLP |
| 3 | 401 | 0.76 | 0.86 | 45 | EVM |
| 4 | 472 | 0.76 | 0.84 | 52 | EVM |
| 5 | 455 | 0.75 | 0.84 | 50 | DSN, PLP |
Interfaces
3 interfaces between chains.
- B–D · 3422 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 3401 Ų buried · 44 hydrogen bonds · protein-protein
- C–B · 745 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6TGH · SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as… · 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 6TGH · PDBe 6TGH · UniProt Q5MCK9
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