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Crystal structure of B30.2 pryspry domain of MID1

Analyse Crystal structure of B30.2 pryspry domain of MID1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QRY
Type: protein
Length: 660 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase midline-1
EC: 2.3.2.27
UniProt: O15344
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	E3 ubiquitin-protein ligase midline-1 (EC 2.3.2.27)	protein	164	2% helix, 49% strand	O15344
B	E3 ubiquitin-protein ligase midline-1 (EC 2.3.2.27)	protein	166	2% helix, 50% strand	O15344
D	E3 ubiquitin-protein ligase midline-1 (EC 2.3.2.27)	protein	166	2% helix, 49% strand	O15344

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	501	0.76	0.84	65	empty
2	690	0.73	0.80	78	empty
3	100	0.46	0.80	28	empty
4	87	0.41	0.78	21	empty
5	51	0.39	0.81	11	empty

Interfaces

5 interfaces between chains.

B–C · 734 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 670 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 454 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 324 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 75 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7QRY · Crystal structure of B30.2 PRYSPRY domain of MID1 · the same entry in another collection · chain A against A, TM-score 1.00
O15344 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase midline-1 (O15344) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O15344
Elsewhere: RCSB PDB 7QRY · PDBe 7QRY · UniProt O15344

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