MolNFT v1 · #131141 · protein

Pandda analysis group deposition -- crystal structure of SP100 after initial refinement with no ligand modelled (structure 11)

5PWO · Nuclear autoantigen sp-100: “Pandda analysis group deposition -- crystal structure of SP100 after initial refinement with no ligand…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.59). MolNFT v1 #131141 on…

PDB: 5PWO
Type: protein
Length: 355 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear autoantigen sp-100
UniProt: P23497
Ligands: ZN
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear autoantigen sp-100	protein	178	50% helix, 5% strand	P23497
B	Nuclear autoantigen sp-100	protein	177	47% helix, 5% strand	P23497

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B

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

Pockets

4 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	229	0.59	0.79	28	MES
2	128	0.41	0.75	18	EDO
3	99	0.35	0.74	16	empty
4	77	0.30	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 537 Å² buried · 7 hydrogen bonds · protein-protein

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 P23497
Elsewhere: RCSB PDB 5PWO · PDBe 5PWO · UniProt P23497

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