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Crystal structure of deph

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

PDB: 4NTE
Type: protein
Length: 588 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deph
UniProt: A4ZPY8
Ligands: FAD, NA, CL
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deph	protein	292	29% helix, 32% strand	A4ZPY8
B	Deph	protein	296	28% helix, 30% strand	A4ZPY8

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 7 copies · chains A, B
CL · Chloride ion · ion · 6 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	999	0.82	0.83	81	FAD, NA, CL
2	1097	0.81	0.82	89	FAD, NA, CL
3	319	0.64	0.80	30	empty
4	62	0.36	0.78	17	empty
5	56	0.28	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 2317 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4NTE · Crystal structure of DepH · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt A4ZPY8
Elsewhere: RCSB PDB 4NTE · PDBe 4NTE · UniProt A4ZPY8

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