MolNFT v1 · #121660 · protein

NVPIZZA2-H16S58 with cobalt

5I1Y · NVPIZZ2A-H16S58: “NVPIZZA2-H16S58 with cobalt”. X-ray diffraction, 2 ligands (CO, SO4), 2 pockets (best druggability 0.71). MolNFT v1 #121660 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I1Y
Type: protein
Length: 257 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NVPIZZ2A-H16S58
Ligands: CO, SO4
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	NVPIZZ2A-H16S58	protein	86	3% helix, 40% strand	—
B	NVPIZZ2A-H16S58	protein	85	7% helix, 42% strand	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	403	0.71	0.82	43	empty
2	69	0.40	0.80	17	empty

Interfaces

3 interfaces between chains.

A–B · 753 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 636 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 516 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5I1Y · NvPizza2-H16S58 with cobalt · 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 5I1Y · PDBe 5I1Y

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