Research workbench

Using molecular dynamics simulations to predict domain swapping of computationally designed protein variants

Analyse Using molecular dynamics simulations to predict domain swapping of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZN8
Type: protein
Length: 192 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Computationally modified engrailed homeodomain
Ligands: K
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Computationally modified engrailed homeodomain	protein	51	71% helix, 0% strand	—
B	Computationally modified engrailed homeodomain	protein	49	73% helix, 0% strand	—
C	Computationally modified engrailed homeodomain	protein	46	76% helix, 0% strand	—
D	Computationally modified engrailed homeodomain	protein	46	80% helix, 0% strand	—

Ligands and binding sites

K · Potassium ion · metal · 4 copies · chains A, D, B, C

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	232	0.82	0.95	24	empty
2	231	0.55	0.78	25	empty
3	258	0.51	0.75	26	empty

Interfaces

6 interfaces between chains.

A–B · 1251 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1122 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 612 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 603 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 272 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

4ZN8 · Using molecular dynamics simulations to predict domain swapping of computationally… · 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 4ZN8 · PDBe 4ZN8

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