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Computationally designed two-component self-assembling tetrahedral cage, T33-21, crystallized in space group R32

Analyse Computationally designed two-component self-assembling tetrahedral cage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NWP
Type: protein
Length: 1,046 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein; Uncharacterized protein
UniProt: O58404, Q9I2D8
Ligands: SO4, NH4
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 62% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative uncharacterized protein	protein	145	75% helix, 0% strand	O58404
B	Putative uncharacterized protein	protein	141	79% helix, 0% strand	O58404
C	Putative uncharacterized protein	protein	140	77% helix, 0% strand	O58404
D	Putative uncharacterized protein	protein	149	72% helix, 1% strand	O58404
E, F, G	Uncharacterized protein	protein	118	29% helix, 33% strand	Q9I2D8
H	Uncharacterized protein	protein	117	28% helix, 33% strand	Q9I2D8

Ligands and binding sites

SO4 · Sulfate ion · ion · 28 copies · chains A, B, C, D, E, F, G, H
NH4 · Ammonium ion · ion · chains H

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

Pockets

5 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	1051	0.72	0.75	104	empty
2	163	0.53	0.80	25	empty
3	297	0.53	0.74	42	empty
4	75	0.37	0.77	20	SO4
5	60	0.27	0.73	15	empty

Interfaces

12 interfaces between chains.

F–G · 1253 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 876 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 777 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 773 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 595 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4NWP · Computationally Designed Two-Component Self-Assembling Tetrahedral Cage, T33-21… · 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
Every structure of UniProt O58404
Every structure of UniProt Q9I2D8
Elsewhere: RCSB PDB 4NWP · PDBe 4NWP · UniProt O58404 · UniProt Q9I2D8

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