MolNFT v1 · #157588 · protein

Pii-like sbtb from cyanobium sp pcc 7001 (apo)

6N4A: “Pii-like sbtb from cyanobium sp pcc 7001 (apo)”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.73). MolNFT v1 #157588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N4A
Type: protein
Length: 508 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pii-like sbtb
UniProt: B5II98
Ligands: PO4
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pii-like sbtb	protein	85	33% helix, 45% strand	B5II98
B	Pii-like sbtb	protein	84	32% helix, 44% strand	B5II98
C, E, F	Pii-like sbtb	protein	85	34% helix, 44% strand	B5II98
D	Pii-like sbtb	protein	84	33% helix, 40% strand	B5II98

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D, E, F

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

Pockets

3 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	759	0.73	0.79	71	PO4
2	100	0.50	0.82	33	PO4
3	106	0.45	0.79	24	empty

Interfaces

11 interfaces between chains.

D–E · 993 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 965 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 937 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 915 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 695 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6N4A · PII-like SbtB from Cyanobium sp PCC 7001 (apo) · 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 B5II98
Elsewhere: RCSB PDB 6N4A · PDBe 6N4A · UniProt B5II98

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.