MolNFT v1 · #102685 · protein
X-ray crystal structure of serine hydroxymethyl transferase from burkholderia cenocepacia bound to plp and serine
4OT8 · Serine hydroxymethyltransferase: “X-ray crystal structure of serine hydroxymethyl transferase from burkholderia cenocepacia bound to plp and…”. X-ray diffraction, 2 ligands (PLP, SER), 11 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 4OT8
- 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, SER
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 414 | 49% helix, 14% strand | B4ECY9 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 411 | 49% helix, 14% strand | B4ECY9 |
| C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 415 | 49% helix, 14% strand | B4ECY9 |
| D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 408 | 49% helix, 14% strand | B4ECY9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, C, B, D
- SER · Serine · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.76 | 0.79 | 112 | PLP, SER |
| 2 | 389 | 0.72 | 0.84 | 46 | SER, PLP |
| 3 | 401 | 0.72 | 0.83 | 46 | SER, PLP |
| 4 | 399 | 0.71 | 0.83 | 59 | PLP, SER |
| 5 | 196 | 0.44 | 0.73 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4321 Ų buried · 61 hydrogen bonds · protein-protein
- B–D · 3846 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 379 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 32 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OT8 · X-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia… · 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 B4ECY9
- Elsewhere: RCSB PDB 4OT8 · PDBe 4OT8 · UniProt B4ECY9
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