Research workbench

Human ddah-1, holo (zn-bound) form

Analyse Human ddah-1, holo (zn-bound) form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7USZ
Type: protein
Length: 560 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
EC: 3.5.3.18
UniProt: O94760
Ligands: ZN, CL
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	274	32% helix, 26% strand	O94760
B	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	286	31% helix, 25% strand	O94760

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains 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	375	0.82	0.91	31	empty
2	407	0.82	0.90	35	empty
3	200	0.66	0.85	32	ZN
4	134	0.62	0.86	28	ZN
5	154	0.39	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 99 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7USZ · Human DDAH-1, holo (Zn-bound) form · 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 7USZ · PDBe 7USZ · UniProt O94760

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