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Crystal structure of human ddah-1

Analyse Crystal structure of human ddah-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SZQ
Type: protein
Length: 1,680 residues
Chains: 6
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
Pockets: 18 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	276	32% helix, 26% strand	O94760
B	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	276	30% helix, 26% strand	O94760
C	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	281	31% helix, 25% strand	O94760
D	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	286	28% helix, 25% strand	O94760
E	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	283	30% helix, 26% strand	O94760
F	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (EC 3.5.3.18)	protein	278	27% helix, 25% strand	O94760

Pockets

18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1014	0.86	0.87	97	empty
2	1029	0.85	0.86	92	empty
3	722	0.82	0.86	64	empty
4	407	0.82	0.90	40	empty
5	433	0.65	0.78	58	empty

Interfaces

9 interfaces between chains.

C–D · 612 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 567 Å² buried · 5 hydrogen bonds · protein-protein
A–F · 400 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 168 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 150 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6SZQ · Crystal structure of human DDAH-1 · the same entry in another collection · chain E against E, 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 6SZQ · PDBe 6SZQ · UniProt O94760

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