MolNFT v1 · #115360 · protein

Crystal structure of NVPIZZA2-S16H58 coordinating a CDCL2 nanocrystal

5CHB: “Crystal structure of NVPIZZA2-S16H58 coordinating a CDCL2 nanocrystal”. X-ray diffraction, 3 ligands (CD, CL, SO4), 2 pockets (best druggability 0.72). MolNFT v1 #115360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CHB
Type: protein
Length: 254 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NVPIZZA2-S16H58
Ligands: CD, CL, SO4
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NVPIZZA2-S16H58	protein	84	4% helix, 40% strand	—
C	NVPIZZA2-S16H58	protein	86	7% helix, 38% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 6 copies · chains A, B, C
CL · Chloride ion · ion · 6 copies · chains B, C
SO4 · Sulfate ion · ion · 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	359	0.72	0.84	42	CD, SO4
2	58	0.34	0.77	16	empty

Interfaces

3 interfaces between chains.

B–C · 668 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 622 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 613 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5CHB · Crystal structure of nvPizza2-S16H58 coordinating a CdCl2 nanocrystal · 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 5CHB · PDBe 5CHB

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