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Crystal structure of human daao in complex with coumpound 13

Analyse Crystal structure of human daao in complex with coumpound 13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3W4K
Type: protein
Length: 1,360 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-amino-acid oxidase
EC: 1.4.3.3
UniProt: P14920
Ligands: FAD, 3LD
Pockets: 19 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	D-amino-acid oxidase (EC 1.4.3.3)	protein	340	33% helix, 28% strand	P14920

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
3LD · 3-hydroxy-6-(2-phenylethyl)pyridazin-4(1H)-one · ligand · 4 copies · chains A, B, C, D

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	560	0.86	0.92	77	FAD, 3LD
2	559	0.86	0.91	80	FAD, 3LD
3	535	0.85	0.90	79	FAD, 3LD
4	795	0.84	0.87	88	FAD, 3LD
5	1088	0.82	0.83	104	empty

Interfaces

6 interfaces between chains.

C–D · 1635 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1592 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 659 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 602 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 62 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3W4K · Crystal Structure of human DAAO in complex with coumpound 13 · the same entry in another collection · chain A against A, TM-score 1.00
P14920 · AlphaFold monomer V2.0 prediction for D-amino-acid oxidase (P14920) · a predicted model of the same protein · chain A 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 P14920
Elsewhere: RCSB PDB 3W4K · PDBe 3W4K · UniProt P14920

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