MolNFT v1 · #70449 · protein

Crystal structure of S. cerevisiae GET4 in complex with an N-terminal fragment of GET5

3LKU · UPF0363 protein YOR164C: “Crystal structure of S. cerevisiae GET4 in complex with an N-terminal fragment of GET5”. X-ray diffraction, 1 ligand (PRO), 7 pockets (best druggability 0.72). MolNFT v1 #70449 on GenesisL1: 3D structure…

PDB: 3LKU
Type: protein
Length: 1,024 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0363 protein YOR164C; Ubiquitin-like protein MDY2
UniProt: Q12125, Q12285
Ligands: PRO
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 67% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UPF0363 protein YOR164C	protein	286	72% helix, 5% strand	Q12125
B	Ubiquitin-like protein MDY2	protein	52	38% helix, 2% strand	Q12285
C	UPF0363 protein YOR164C	protein	290	73% helix, 4% strand	Q12125
D	Ubiquitin-like protein MDY2	protein	51	33% helix, 2% strand	Q12285
E	UPF0363 protein YOR164C	protein	291	73% helix, 4% strand	Q12125
F	Ubiquitin-like protein MDY2	protein	54	39% helix, 2% strand	Q12285

Ligands and binding sites

PRO · Proline · ligand · 2 copies · chains A, E

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	901	0.72	0.76	97	empty
2	140	0.51	0.79	18	empty
3	105	0.45	0.78	20	empty
4	173	0.42	0.74	25	empty
5	78	0.38	0.77	17	empty

Interfaces

7 interfaces between chains.

E–F · 2613 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2569 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2564 Å² buried · 28 hydrogen bonds · protein-protein
C–E · 270 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 213 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 modified (engineered).

Compared structures

3LKU · Crystal structure of S. cerevisiae Get4 in complex with an N-terminal fragment of Get5 · the same entry in another collection · chain F against F, TM-score 1.00
Q12125 · AlphaFold monomer V2.0 prediction for golgi to er traffic protein 4 (Q12125) · a predicted model of the same protein · chain C against A, TM-score 0.98
Q12285 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein MDY2 (Q12285) · a predicted model of the same protein · chain B against A, TM-score 0.52

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 Q12125
Every structure of UniProt Q12285
Elsewhere: RCSB PDB 3LKU · PDBe 3LKU · UniProt Q12125 · UniProt Q12285

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