MolNFT v1 · #109946 · protein

Structure of a phospholipid trafficking complex, native

4XHR · Protein UPS1, mitochondrial: “Structure of a phospholipid trafficking complex, native”. X-ray diffraction, 8 pockets (best druggability 0.86). MolNFT v1 #109946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XHR
Type: protein
Length: 482 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein UPS1, mitochondrial; Mitochondrial distribution and morphology protein 35
UniProt: Q05776, O60200
Pockets: 8 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein UPS1, mitochondrial	protein	170	25% helix, 41% strand	Q05776
N	Mitochondrial distribution and morphology protein 35	protein	71	63% helix, 0% strand	O60200
M	Mitochondrial distribution and morphology protein 35	protein	71	63% helix, 0% strand	O60200

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	532	0.86	0.92	61	empty
2	874	0.83	0.85	88	empty
3	86	0.55	0.85	16	empty
4	153	0.51	0.79	23	empty
5	107	0.49	0.80	15	empty

Interfaces

4 interfaces between chains.

A–N · 1420 Å² buried · 15 hydrogen bonds · protein-protein
B–M · 1402 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 240 Å² buried · 0 hydrogen bonds · protein-protein
N–B · 230 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4XHR · Structure of a phospholipid trafficking complex, native · the same entry in another collection · chain A against A, TM-score 1.00
Q05776 · AlphaFold monomer V2.0 prediction for protein UPS1, mitochondrial (Q05776) · a predicted model of the same protein · chain A against A, TM-score 0.97
O60200 · AlphaFold monomer V2.0 prediction for mitochondrial distribution and morphology protein… · a predicted model of the same protein · chain N against A, TM-score 0.86

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 Q05776
Every structure of UniProt O60200
Elsewhere: RCSB PDB 4XHR · PDBe 4XHR · UniProt Q05776 · UniProt O60200

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