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Crystal structure of UPS1-MDM35 complex with pa

Analyse Crystal structure of UPS1-MDM35 complex with pa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YTX
Type: protein
Length: 1,892 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial distribution and morphology protein 35; Protein UPS1, mitochondrial
UniProt: O60200, Q05776
Ligands: PX2
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 9 distinct chains · 30% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M	Mitochondrial distribution and morphology protein 35	protein	73	59% helix, 1% strand	O60200
B	Protein UPS1, mitochondrial	protein	160	21% helix, 42% strand	Q05776
D	Protein UPS1, mitochondrial	protein	170	26% helix, 38% strand	Q05776
F	Protein UPS1, mitochondrial	protein	167	30% helix, 40% strand	Q05776
H	Protein UPS1, mitochondrial	protein	162	18% helix, 39% strand	Q05776
J, L	Protein UPS1, mitochondrial	protein	169	28% helix, 40% strand	Q05776
N	Protein UPS1, mitochondrial	protein	157	30% helix, 41% strand	Q05776
O	Mitochondrial distribution and morphology protein 35	protein	68	66% helix, 0% strand	O60200
P	Protein UPS1, mitochondrial	protein	159	28% helix, 44% strand	Q05776

Ligands and binding sites

PX2 · 1,2-dilauroyl-sn-glycero-3-phosphate · ligand · 2 copies · chains B, N, D, F

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	923	0.81	0.82	64	PX2
2	871	0.78	0.81	75	empty
3	787	0.76	0.80	63	PX2
4	596	0.75	0.81	54	empty
5	573	0.74	0.82	53	empty

Interfaces

24 interfaces between chains.

D–F · 1971 Å² buried · 10 hydrogen bonds · protein-protein
J–L · 1878 Å² buried · 8 hydrogen bonds · protein-protein
H–P · 1623 Å² buried · 4 hydrogen bonds · protein-protein
B–N · 1603 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1433 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4YTX · Crystal structure of Ups1-Mdm35 complex with PA · the same entry in another collection · chain K against K, 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 O60200
Every structure of UniProt Q05776
Elsewhere: RCSB PDB 4YTX · PDBe 4YTX · UniProt O60200 · UniProt Q05776

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