MolNFT v1 · #13917 · protein
Crystal structure of the complex between rabbit cytosolic serine hydroxymethyltransferase and triglu-5-formyl-tetrahydrofolate
1LS3: “Crystal structure of the complex between rabbit cytosolic serine hydroxymethyltransferase and…”. X-ray diffraction, 3 ligands (PLP, GLY, TGF), 20 pockets (best druggability 0.79). MolNFT v1 #13917 on GenesisL1: 3D structure, binding…
- PDB
- 1LS3
- Type
- protein
- Length
- 1,841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- P07511
- Ligands
- PLP, GLY, TGF
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 465 | 49% helix, 13% strand | P07511 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 455 | 48% helix, 13% strand | P07511 |
| C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 465 | 49% helix, 14% strand | P07511 |
| D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 456 | 47% helix, 13% strand | P07511 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- GLY · Glycine · ligand · 2 copies · chains A, B, C, D
- TGF · 2-[4-(4-{4-[(2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydro-pteridin-6-ylmethyl)-amino]-benzoylamino}-4-carboxy-butyrylam ino)-4-carboxy-butyrylamino]-pentanedioic acid · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.79 | 0.98 | 34 | empty |
| 2 | 89 | 0.78 | 0.99 | 16 | empty |
| 3 | 648 | 0.75 | 0.81 | 95 | GLY, PLP |
| 4 | 385 | 0.74 | 0.84 | 45 | PLP, GLY |
| 5 | 469 | 0.73 | 0.82 | 63 | TGF |
Interfaces
6 interfaces between chains.
- A–B · 4671 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 4592 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 917 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 906 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1LS3 · Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase… · the same entry in another collection · chain D against D, TM-score 1.00
- P07511 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, cytosolic (P07511) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P07511
- Elsewhere: RCSB PDB 1LS3 · PDBe 1LS3 · UniProt P07511
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