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Crystal structure of app peptide bound rat MINT2 parm

Analyse Crystal structure of app peptide bound rat MINT2 parm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SV1
Type: protein
Length: 484 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloid beta A4 precursor protein-binding family a member 2; Amyloid beta A4 protein
UniProt: O35431, P05067
Pockets: 5 · best druggability 0.42

Structure

x-ray diffraction · 6 distinct chains · 32% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Amyloid beta A4 precursor protein-binding family a member 2	protein	163	36% helix, 33% strand	O35431
B	Amyloid beta A4 precursor protein-binding family a member 2	protein	143	34% helix, 34% strand	O35431
C	Amyloid beta A4 precursor protein-binding family a member 2	protein	150	30% helix, 36% strand	O35431
D	Amyloid beta A4 protein	protein	14	36% helix, 21% strand	P05067
E	Amyloid beta A4 protein	protein	11	0% helix, 9% strand	P05067
F	Amyloid beta A4 protein	protein	3	0% helix, 0% strand	P05067

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.42	0.77	21	empty
2	98	0.40	0.77	23	empty
3	56	0.28	0.74	10	empty
4	65	0.28	0.73	17	empty
5	65	0.27	0.73	15	empty

Interfaces

5 interfaces between chains.

A–D · 806 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 672 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 618 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 610 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 151 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3SV1 · Crystal structure of APP peptide bound rat Mint2 PARM · the same entry in another collection · chain F against F, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain F against A, TM-score 1.00
O35431 · AlphaFold monomer V2.0 prediction for amyloid-beta A4 precursor protein-binding family a… · a predicted model of the same protein · chain B against A, TM-score 0.95

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 O35431
Every structure of UniProt P05067
Elsewhere: RCSB PDB 3SV1 · PDBe 3SV1 · UniProt O35431 · UniProt P05067

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