MolNFT v1 · #123639 · protein

Crystal structure of phosphatidic acid transporter UPS1/MDM35 void of bound phospholipid from saccharomyces cerevisiae at 2.9 ångströms resolution

5JQL · Protein UPS1, mitochondrial: “Crystal structure of phosphatidic acid transporter UPS1/MDM35 void of bound phospholipid from saccharomyces…”. X-ray diffraction, 20 pockets (best druggability 0.87). MolNFT v1 #123639 on GenesisL1: 3D…

PDB: 5JQL
Type: protein
Length: 1,432 residues
Chains: 12
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: 20 · best druggability 0.87

Structure

x-ray diffraction · 9 distinct chains · 36% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein UPS1, mitochondrial	protein	171	25% helix, 46% strand	Q05776
B, F	Mitochondrial distribution and morphology protein 35	protein	72	67% helix, 0% strand	O60200
D	Mitochondrial distribution and morphology protein 35	protein	74	64% helix, 0% strand	O60200
E	Protein UPS1, mitochondrial	protein	166	27% helix, 47% strand	Q05776
G	Protein UPS1, mitochondrial	protein	169	25% helix, 47% strand	Q05776
H	Mitochondrial distribution and morphology protein 35	protein	71	68% helix, 0% strand	O60200
I	Protein UPS1, mitochondrial	protein	160	28% helix, 46% strand	Q05776
J, L	Mitochondrial distribution and morphology protein 35	protein	71	68% helix, 0% strand	O60200
K	Protein UPS1, mitochondrial	protein	164	24% helix, 46% strand	Q05776

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	822	0.87	0.90	98	empty
2	919	0.87	0.89	118	empty
3	595	0.85	0.90	70	empty
4	541	0.85	0.91	58	empty
5	577	0.84	0.90	70	empty

Interfaces

28 interfaces between chains.

C–G · 2213 Å² buried · 3 hydrogen bonds · protein-protein
E–I · 2150 Å² buried · 3 hydrogen bonds · protein-protein
A–K · 2081 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 1492 Å² buried · 16 hydrogen bonds · protein-protein
K–L · 1466 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 modified, 12 disulfide (engineered, disulfide).

Compared structures

5JQL · Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid… · 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 Q05776
Every structure of UniProt O60200
Elsewhere: RCSB PDB 5JQL · PDBe 5JQL · UniProt Q05776 · UniProt O60200

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