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Crystal structure of a probable dehydrogenase protein

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

PDB: 4FGS
Type: protein
Length: 936 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable dehydrogenase protein
UniProt: Q2KC28
Ligands: SO4
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable dehydrogenase protein	protein	240	47% helix, 19% strand	Q2KC28
B	Probable dehydrogenase protein	protein	228	44% helix, 20% strand	Q2KC28
C	Probable dehydrogenase protein	protein	234	46% helix, 19% strand	Q2KC28
D	Probable dehydrogenase protein	protein	234	47% helix, 19% strand	Q2KC28

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	945	0.83	0.85	64	empty
2	258	0.63	0.82	50	empty
3	273	0.63	0.81	47	SO4
4	216	0.56	0.79	35	empty
5	135	0.54	0.82	34	SO4

Interfaces

6 interfaces between chains.

C–D · 1611 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1609 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1478 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1425 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 134 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

4FGS · Crystal structure of a probable dehydrogenase protein · 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 Q2KC28
Elsewhere: RCSB PDB 4FGS · PDBe 4FGS · UniProt Q2KC28

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