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A yidc-like protein in the archaeal plasma membrane

Analyse A yidc-like protein in the archaeal plasma membrane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C8J
Type: protein
Length: 2,308 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody fragment, heavy chain; Antibody fragment, light chain; Protein MJ0480
UniProt: Q57904
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 9 distinct chains · 21% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Antibody fragment, heavy chain	protein	229	6% helix, 51% strand	—
B	Antibody fragment, light chain	protein	214	5% helix, 48% strand	—
C	Antibody fragment, heavy chain	protein	230	7% helix, 49% strand	—
D	Antibody fragment, light chain	protein	212	5% helix, 50% strand	—
E	Antibody fragment, heavy chain	protein	230	7% helix, 49% strand	—
F, H	Antibody fragment, light chain	protein	213	5% helix, 48% strand	—
I, J	Protein MJ0480	protein	134	69% helix, 2% strand	Q57904
K	Protein MJ0480	protein	133	68% helix, 2% strand	Q57904
L	Protein MJ0480	protein	137	69% helix, 3% strand	Q57904

Ligands and binding sites

LMT · Dodecyl-beta-D-maltoside · additive · chains L

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1155	0.79	0.80	113	empty
2	895	0.76	0.78	86	empty
3	242	0.69	0.85	34	empty
4	183	0.68	0.86	28	empty
5	224	0.66	0.84	33	empty

Interfaces

17 interfaces between chains.

I–L · 2967 Å² buried · 9 hydrogen bonds · protein-protein
J–K · 2964 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1916 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1878 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1804 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide (disulfide).

Compared structures

5C8J · A YidC-like protein in the archaeal plasma membrane · the same entry in another collection · chain L against L, 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 Q57904
Elsewhere: RCSB PDB 5C8J · PDBe 5C8J · UniProt Q57904

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