MolNFT v1 · #171060 · protein
Shmt from streptococcus thermophilus TYR55SER variant as internal aldimine and as non-covalent complex with D-ser
6YRW · Serine hydroxymethyltransferase: “Shmt from streptococcus thermophilus TYR55SER variant as internal aldimine and as non-covalent complex with…”. X-ray diffraction, 2 ligands (PLP, DSN), 20 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 6YRW
- 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
- PLP, DSN
- Pockets
- 20 · best druggability 0.80
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
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- DSN · D-serine · ligand · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.80 | 0.81 | 90 | GOL |
| 2 | 404 | 0.74 | 0.84 | 50 | PLP, DSN |
| 3 | 404 | 0.74 | 0.84 | 53 | PLP, DSN |
| 4 | 316 | 0.71 | 0.84 | 29 | DSN |
| 5 | 349 | 0.70 | 0.83 | 32 | DSN |
Interfaces
3 interfaces between chains.
- A–C · 3420 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 3418 Ų buried · 48 hydrogen bonds · protein-protein
- C–B · 797 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6YRW · SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as… · the same entry in another collection · chain B against B, 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 6YRW · PDBe 6YRW · UniProt Q5MCK9
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