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Crystal structure of S.CEREVISIAE IST1 N-terminal domain in complex with DID2 mim motif

Analyse Crystal structure of S.CEREVISIAE IST1 N-terminal domain in complex with DID2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GGZ
Type: protein
Length: 810 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Increased sodium tolerance protein 1; Vacuolar protein-sorting-associated protein 46
UniProt: P53843, P69771
Pockets: 16 · best druggability 0.73

Structure

x-ray diffraction · 7 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Increased sodium tolerance protein 1	protein	186	72% helix, 0% strand	P53843
B	Increased sodium tolerance protein 1	protein	186	72% helix, 0% strand	P53843
C	Increased sodium tolerance protein 1	protein	182	73% helix, 0% strand	P53843
D	Increased sodium tolerance protein 1	protein	188	72% helix, 0% strand	P53843
E, F	Vacuolar protein-sorting-associated protein 46	protein	17	65% helix, 0% strand	P69771
G	Vacuolar protein-sorting-associated protein 46	protein	16	44% helix, 0% strand	P69771
H	Vacuolar protein-sorting-associated protein 46	protein	18	61% helix, 0% strand	P69771

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	59	0.73	0.98	15	empty
2	51	0.73	0.99	17	empty
3	57	0.72	0.98	18	empty
4	349	0.66	0.80	40	empty
5	353	0.64	0.79	37	empty

Interfaces

10 interfaces between chains.

A–B · 843 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 823 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 721 Å² buried · 7 hydrogen bonds · protein-protein
C–G · 656 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 647 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3GGZ · Crystal Structure of S.cerevisiae Ist1 N-terminal domain in complex with Did2 MIM motif · the same entry in another collection · chain H against H, TM-score 1.00
P53843 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein IST1… · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P53843
Every structure of UniProt P69771
Elsewhere: RCSB PDB 3GGZ · PDBe 3GGZ · UniProt P53843 · UniProt P69771

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