MolNFT v1 · #161098 · protein

Arabidopsis OM64 tpr domain

6Q3Q · Outer envelope protein 64, mitochondrial: “Arabidopsis OM64 tpr domain”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.75). MolNFT v1 #161098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Q3Q
Type: protein
Length: 258 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer envelope protein 64, mitochondrial; Gly-ser-lys-met-glu-glu-val-asp
UniProt: F4KCL7
Ligands: SO4
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Outer envelope protein 64, mitochondrial	protein	121	76% helix, 0% strand	F4KCL7
a, b	Gly-ser-lys-met-glu-glu-val-asp	protein	8	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, a, B, b
GOL · Glycerol · additive · 7 copies · chains A, B, b, a

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	434	0.75	0.85	66	GOL

Interfaces

5 interfaces between chains.

A–B · 647 Å² buried · 5 hydrogen bonds · protein-protein
A–a · 506 Å² buried · 13 hydrogen bonds · protein-protein
B–b · 504 Å² buried · 13 hydrogen bonds · protein-protein
B–a · 68 Å² buried · 1 hydrogen bond · protein-protein
A–b · 63 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6Q3Q · Arabidopsis OM64 TPR domain · the same entry in another collection · chain A against A, TM-score 1.00
F4KCL7 · AlphaFold monomer V2.0 prediction for outer envelope protein 64, mitochondrial (F4KCL7) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 F4KCL7
Elsewhere: RCSB PDB 6Q3Q · PDBe 6Q3Q · UniProt F4KCL7

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