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Crystal structure of zntb cytoplasmic domain from vibrio parahaemolyticus rimd 2210633

Analyse Crystal structure of zntb cytoplasmic domain from vibrio parahaemolyticus rimd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CK6
Type: protein
Length: 1,219 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative membrane transport protein
UniProt: Q87M69
Ligands: CL
Pockets: 20 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Putative membrane transport protein	protein	244	52% helix, 16% strand	Q87M69
C	Putative membrane transport protein	protein	242	51% helix, 17% strand	Q87M69
E	Putative membrane transport protein	protein	245	51% helix, 16% strand	Q87M69

Ligands and binding sites

CL · Chloride ion · ion · 25 copies · chains A, B, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	482	0.63	0.76	42	empty
2	351	0.58	0.76	47	empty
3	280	0.57	0.77	37	CL
4	262	0.56	0.77	44	CL
5	307	0.55	0.75	38	empty

Interfaces

5 interfaces between chains.

D–E · 1149 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 1133 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1128 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1120 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1111 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 modified (engineered).

Compared structures

3CK6 · Crystal structure of ZntB cytoplasmic domain from Vibrio parahaemolyticus RIMD 2210633 · 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 Q87M69
Elsewhere: RCSB PDB 3CK6 · PDBe 3CK6 · UniProt Q87M69

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