MolNFT v1 · #102698 · protein
X-ray crystal structure of serine hydroxymethyl transferase from burkholderia cenocepacia bound to plp and glycine
4OTL · Serine hydroxymethyltransferase: “X-ray crystal structure of serine hydroxymethyl transferase from burkholderia cenocepacia bound to plp and…”. X-ray diffraction, 2 ligands (PLP, GLY), 17 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 4OTL
- Type
- protein
- Length
- 1,648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- B4ECY9
- Ligands
- PLP, GLY
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 409 | 50% helix, 14% strand | B4ECY9 |
| C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 414 | 50% helix, 14% strand | B4ECY9 |
| D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 416 | 49% helix, 13% strand | B4ECY9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- GLY · Glycine · ligand · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.74 | 0.85 | 43 | PLP, GLY |
| 2 | 344 | 0.72 | 0.84 | 46 | PLP, GLY |
| 3 | 356 | 0.72 | 0.84 | 42 | PLP, GLY |
| 4 | 58 | 0.68 | 0.96 | 27 | PLP |
| 5 | 309 | 0.67 | 0.82 | 26 | GLY |
Interfaces
3 interfaces between chains.
- B–D · 4174 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 4077 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 384 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4OTL · X-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia… · the same entry in another collection · chain C against C, 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 B4ECY9
- Elsewhere: RCSB PDB 4OTL · PDBe 4OTL · UniProt B4ECY9
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