MolNFT v1 · #9619 · protein

Crystal structure of csdb complexed with L-propargylglycine

1I29: “Crystal structure of csdb complexed with L-propargylglycine”. X-ray diffraction, 2 ligands (LPG, PLP), 2 pockets (best druggability 0.54). MolNFT v1 #9619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1I29
Type: protein
Length: 405 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Csdb
EC: 4.4.1.16
Ligands: LPG, PLP
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Csdb (EC 4.4.1.16)	protein	405	43% helix, 19% strand	—

Ligands and binding sites

LPG · (2S)-2-aminobut-3-ynoic acid · ligand · chains A
PLP · Pyridoxal-5'-phosphate · ligand · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.54	0.83	21	empty
2	147	0.52	0.80	27	LPG, PLP

Compared structures

1I29 · Crystal structure of csdb complexed with L-propargylglycine · 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
Elsewhere: RCSB PDB 1I29 · PDBe 1I29

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