Research workbench
Apo-shmt from streptococcus thermophilus TYR55SER variant in complex with D-threonine
Analyse Apo-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
- 6TI3
- 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
- DTH, NA
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 410 | 48% helix, 13% strand | Q5MCK9 |
Ligands and binding sites
- DTH · D-threonine · ligand · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · chains D
- GOL · Glycerol · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.82 | 0.83 | 86 | GOL |
| 2 | 507 | 0.78 | 0.86 | 52 | DTH |
| 3 | 489 | 0.78 | 0.85 | 51 | DTH |
| 4 | 483 | 0.77 | 0.85 | 51 | DTH |
| 5 | 487 | 0.76 | 0.84 | 49 | DTH |
Interfaces
3 interfaces between chains.
- B–D · 3376 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 3358 Ų buried · 53 hydrogen bonds · protein-protein
- C–B · 786 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6TI3 · Apo-SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with D-Threonine · 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 6TI3 · PDBe 6TI3 · UniProt Q5MCK9
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