MolNFT v1 · #121249 · protein

A circularly permuted pdua forming an icosahedral cage

5HPN: “A circularly permuted pdua forming an icosahedral cage”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.58). MolNFT v1 #121249 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HPN
Type: protein
Length: 424 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Permuted pdua
Ligands: SO4
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Permuted pdua	protein	87	44% helix, 36% strand	—
B	Permuted pdua	protein	84	40% helix, 36% strand	—
C	Permuted pdua	protein	85	44% helix, 35% strand	—
D	Permuted pdua	protein	81	43% helix, 33% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A, B, C, D, E

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

Pockets

2 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	77	0.58	0.88	21	empty
2	175	0.50	0.78	23	SO4

Interfaces

5 interfaces between chains.

B–C · 831 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 814 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 797 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 778 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 752 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5HPN · A circularly permuted PduA forming an icosahedral cage · 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 5HPN · PDBe 5HPN

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