GL1X · GenesisL1 explorer

MolNFT v1 · #139029 · protein

Crystal structure of human serine racemase

5X2L: “Crystal structure of human serine racemase”. X-ray diffraction, 2 ligands (PLP, MG), 2 pockets (best druggability 0.66). MolNFT v1 #139029 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5X2L
Type
protein
Length
612 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Serine racemase
EC
5.1.1.18, 4.3.1.18, 4.3.1.17
UniProt
Q9GZT4
Ligands
PLP, MG
Pockets
2 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ASerine racemase (EC 5.1.1.18, 4.3.1.18, 4.3.1.17)protein30550% helix, 16% strandQ9GZT4
BSerine racemase (EC 5.1.1.18, 4.3.1.18, 4.3.1.17)protein30750% helix, 16% strandQ9GZT4

Ligands and binding sites

  • PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
  • MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15850.660.7669PLP
25390.650.7663PLP

Interfaces

1 interface between chains.

  • A–B · 200 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

  • 5X2L · Crystal Structure of Human Serine Racemase · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9GZT4 · AlphaFold monomer V2.0 prediction for serine racemase (Q9GZT4) · a predicted model of the same protein · chain A against A, TM-score 0.96

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