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Crystal structure of de novo designed MID1-zinc

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

PDB: 3V1C
Type: protein
Length: 93 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Computational design, MID1-zinc
Ligands: UNL, ZN
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Computational design, MID1-zinc	protein	46	80% helix, 0% strand	—
B	Computational design, MID1-zinc	protein	47	74% helix, 0% strand	—

Ligands and binding sites

UNL · Unknown ligand · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A, B
TLA · L(+)-tartaric acid · additive · chains A, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.39	0.80	14	TLA
2	55	0.34	0.78	12	empty

Interfaces

1 interface between chains.

A–B · 613 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3V1C · Crystal structure of de novo designed MID1-zinc · 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 3V1C · PDBe 3V1C

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