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Crystal structure of a de novo designed protein homodimer with curved beta-sheet

Analyse Crystal structure of a de novo designed protein homodimer with curved beta-sheet in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TPH
Type: protein
Length: 241 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: De novo NTF2 homodimer
Ligands: CL
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	De novo NTF2 homodimer	protein	120	37% helix, 44% strand	—
B	De novo NTF2 homodimer	protein	121	36% helix, 45% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

4 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	298	0.71	0.84	42	PEG
2	169	0.52	0.79	30	empty
3	88	0.38	0.76	14	empty
4	98	0.37	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1026 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5TPH · Crystal structure of a de novo designed protein homodimer with curved beta-sheet · 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 5TPH · PDBe 5TPH

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