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Crystal structure of de novo designed MID1-zinc H35E mutant

Analyse Crystal structure of de novo designed MID1-zinc H35E mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3V1F
Type: protein
Length: 86 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Computational design, MID1-zinc H35E mutant
Ligands: ZN
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Computational design, MID1-zinc H35E mutant	protein	44	86% helix, 0% strand	—
B	Computational design, MID1-zinc H35E mutant	protein	42	86% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A
ACT · Acetate ion · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	122	0.50	0.80	23	empty
2	67	0.50	0.84	13	empty

Interfaces

1 interface between chains.

A–B · 551 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3V1F · Crystal structure of de novo designed MID1-zinc H35E mutant · the same entry in another collection · chain A 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
Elsewhere: RCSB PDB 3V1F · PDBe 3V1F

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