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Structure of NVPIZZA2-H16S58

Analyse Structure of NVPIZZA2-H16S58 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I1Z
Type: protein
Length: 1,525 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NVPIZZA2-H16S58
Ligands: SO4
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F, G, J, L, P	NVPIZZA2-H16S58	protein	85	4% helix, 40% strand	—
C, E, I, K, N, R	NVPIZZA2-H16S58	protein	84	4% helix, 38% strand	—
H	NVPIZZA2-H16S58	protein	83	4% helix, 43% strand	—
M, O, Q	NVPIZZA2-H16S58	protein	86	3% helix, 40% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, F, J, D, E, G, H, I, L, K, M, P, N, O, R, Q

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

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	847	0.81	0.84	102	SO4
2	903	0.80	0.83	93	empty
3	232	0.73	0.89	49	SO4
4	499	0.73	0.82	47	empty
5	219	0.73	0.89	41	SO4

Interfaces

41 interfaces between chains.

M–P · 788 Å² buried · 7 hydrogen bonds · protein-protein
P–Q · 767 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 764 Å² buried · 7 hydrogen bonds · protein-protein
G–J · 742 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 728 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5I1Z · Structure of nvPizza2-H16S58 · 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 5I1Z · PDBe 5I1Z

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