MolNFT v1 · #142960 · protein

Crystal structure of E. COLI yidc at 2.8 a resolution

6AL2 · Membrane protein insertase yidc: “Crystal structure of E. COLI yidc at 2.8 a resolution”. X-ray diffraction, 8 pockets (best druggability 0.81). MolNFT v1 #142960 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6AL2
Type: protein
Length: 964 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Membrane protein insertase yidc
UniProt: B7MGC7
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Membrane protein insertase yidc	protein	484	37% helix, 29% strand	B7MGC7
B	Membrane protein insertase yidc	protein	480	35% helix, 30% strand	B7MGC7

Ligands and binding sites

OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A

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

Pockets

8 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	743	0.81	0.84	53	OLC
2	768	0.80	0.83	58	empty
3	742	0.76	0.81	53	empty
4	851	0.71	0.76	63	empty
5	279	0.53	0.75	36	empty

Interfaces

1 interface between chains.

A–B · 212 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6AL2 · Crystal structure of E. coli YidC at 2.8 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
B7MGC7 · AlphaFold monomer V2.0 prediction for membrane protein insertase yidc (B7MGC7) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 B7MGC7
Elsewhere: RCSB PDB 6AL2 · PDBe 6AL2 · UniProt B7MGC7

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