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Co-crystal structure of PD_DINASE with probe glycine-propargylglycine- aomk

Analyse Co-crystal structure of PD_DINASE with probe glycine-propargylglycine- aomk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W4N
Type: protein
Length: 2,124 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminopeptidase
UniProt: A0A395YY96
Ligands: SWJ, K
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aminopeptidase	protein	347	37% helix, 20% strand	A0A395YY96
B	Aminopeptidase	protein	350	37% helix, 19% strand	A0A395YY96
C	Aminopeptidase	protein	347	37% helix, 20% strand	A0A395YY96
D	Aminopeptidase	protein	351	37% helix, 20% strand	A0A395YY96
E	Aminopeptidase	protein	366	37% helix, 19% strand	A0A395YY96
F	Aminopeptidase	protein	363	39% helix, 19% strand	A0A395YY96

Ligands and binding sites

SWJ · 2-azanyl-~{N}-[(3~{S})-2-oxidanylidenehex-5-yn-3-yl]ethanamide · ligand · 6 copies · chains A, B, C, D, E, F
K · Potassium ion · metal · 12 copies · chains A, B, C, D, E, F

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.80	0.81	136	SWJ
2	843	0.78	0.81	96	SWJ
3	633	0.74	0.81	63	empty
4	237	0.63	0.82	50	SWJ
5	159	0.59	0.83	36	SWJ

Interfaces

6 interfaces between chains.

A–F · 1506 Å² buried · 20 hydrogen bonds · protein-protein
D–E · 1487 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1481 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1183 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1163 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 covalent (covalent ligand).

Compared structures

6W4N · Co-crystal structure of Pd_dinase with probe glycine-propargylglycine-AOMK · 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
Every structure of UniProt A0A395YY96
Elsewhere: RCSB PDB 6W4N · PDBe 6W4N · UniProt A0A395YY96

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