MolNFT v1 · #41011 · protein

DDAH1 complexed with L-257

2JAJ · Ng, ng-dimethylarginine dimethylaminohydrolase 1: “DDAH1 complexed with L-257”. X-ray diffraction, 1 ligand (D20), 5 pockets (best druggability 0.82). MolNFT v1 #41011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2JAJ
Type: protein
Length: 553 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ng, ng-dimethylarginine dimethylaminohydrolase 1
EC: 3.5.3.18
UniProt: O94760
Ligands: D20
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ng, ng-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	272	32% helix, 26% strand	O94760
B	Ng, ng-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	281	28% helix, 26% strand	O94760

Ligands and binding sites

D20 · N~5~-{imino[(2-methoxyethyl)amino]methyl}-L-ornithine · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.82	0.91	31	empty
2	375	0.81	0.90	32	empty
3	122	0.61	0.87	26	D20
4	178	0.57	0.81	28	D20
5	52	0.40	0.82	21	empty

Interfaces

1 interface between chains.

A–B · 482 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2JAJ · DDAH1 complexed with L-257 · the same entry in another collection · chain A against A, TM-score 1.00
O94760 · AlphaFold monomer V2.0 prediction for N(G),N(G)-dimethylarginine dimethylaminohydrolase 1… · 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 O94760
Elsewhere: RCSB PDB 2JAJ · PDBe 2JAJ · UniProt O94760

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