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Crystal structure of YPP1

Analyse Crystal structure of YPP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N5C
Type: protein
Length: 5,903 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cargo-transport protein YPP1
UniProt: P46951
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cargo-transport protein YPP1	protein	745	73% helix, 0% strand	P46951
B	Cargo-transport protein YPP1	protein	741	72% helix, 0% strand	P46951
C	Cargo-transport protein YPP1	protein	737	73% helix, 0% strand	P46951
D	Cargo-transport protein YPP1	protein	757	73% helix, 1% strand	P46951
E	Cargo-transport protein YPP1	protein	727	73% helix, 0% strand	P46951
F	Cargo-transport protein YPP1	protein	727	73% helix, 0% strand	P46951
G	Cargo-transport protein YPP1	protein	735	72% helix, 0% strand	P46951
H	Cargo-transport protein YPP1	protein	734	73% helix, 0% strand	P46951

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	928	0.82	0.84	92	empty
2	827	0.78	0.81	63	empty
3	974	0.78	0.80	67	empty
4	1139	0.77	0.79	104	empty
5	888	0.77	0.80	89	empty

Interfaces

11 interfaces between chains.

D–H · 1083 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 869 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 685 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 626 Å² buried · 1 hydrogen bond · protein-protein
E–F · 528 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 129 modified (engineered).

Compared structures

4N5C · Crystal structure of Ypp1 · the same entry in another collection · chain H against H, TM-score 1.00
P46951 · AlphaFold monomer V2.0 prediction for cargo-transport protein YPP1 (P46951) · a predicted model of the same protein · chain D against A, 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 P46951
Elsewhere: RCSB PDB 4N5C · PDBe 4N5C · UniProt P46951

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