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Crystal structure of a functionally unknown protein from eubacterium ventriosum atcc 27560

Analyse Crystal structure of a functionally unknown protein from eubacterium ventriosum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G74
Type: protein
Length: 707 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein of unknown function
UniProt: A5Z9E1
Ligands: SO4
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 7 distinct chains · 26% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein of unknown function	protein	87	25% helix, 45% strand	A5Z9E1
B	Protein of unknown function	protein	90	26% helix, 44% strand	A5Z9E1
C	Protein of unknown function	protein	88	24% helix, 42% strand	A5Z9E1
D, E	Protein of unknown function	protein	92	24% helix, 41% strand	A5Z9E1
F	Protein of unknown function	protein	86	28% helix, 43% strand	A5Z9E1
G	Protein of unknown function	protein	87	26% helix, 41% strand	A5Z9E1
H	Protein of unknown function	protein	85	27% helix, 44% strand	A5Z9E1

Ligands and binding sites

SO4 · Sulfate ion · ion · 17 copies · chains A, D, B, E, C, F, H, G

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	740	0.78	0.82	101	SO4
2	553	0.75	0.83	68	SO4
3	419	0.74	0.84	48	empty
4	239	0.71	0.87	37	empty
5	290	0.66	0.82	45	empty

Interfaces

20 interfaces between chains.

C–D · 706 Å² buried · 7 hydrogen bonds · protein-protein
E–H · 631 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 625 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 619 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 613 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 modified (engineered).

Compared structures

3G74 · Crystal structure of a functionally unknown protein from Eubacterium ventriosum ATCC 27560 · 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 A5Z9E1
Elsewhere: RCSB PDB 3G74 · PDBe 3G74 · UniProt A5Z9E1

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