MolNFT v1 · #97544 · protein

Structure of the SPT16D POB3N heterodimer

4KHB · Uncharacterized protein SPT16D: “Structure of the SPT16D POB3N heterodimer”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.76). MolNFT v1 #97544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4KHB
Type: protein
Length: 1,118 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein SPT16D; Uncharacterized protein POB3N
UniProt: G0SDN1, G0SHK5
Ligands: SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 18% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein SPT16D	protein	113	29% helix, 37% strand	G0SDN1
D	Uncharacterized protein POB3N	protein	170	11% helix, 51% strand	G0SHK5
F	Uncharacterized protein POB3N	protein	173	11% helix, 48% strand	G0SHK5
H	Uncharacterized protein POB3N	protein	168	11% helix, 52% strand	G0SHK5
G	Uncharacterized protein SPT16D	protein	106	29% helix, 40% strand	G0SDN1
E	Uncharacterized protein SPT16D	protein	106	27% helix, 42% strand	G0SDN1
C	Uncharacterized protein SPT16D	protein	106	28% helix, 40% strand	G0SDN1
B	Uncharacterized protein POB3N	protein	176	11% helix, 49% strand	G0SHK5

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, D, F, H, E, C, B

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

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	799	0.76	0.80	100	empty
2	439	0.66	0.79	52	empty
3	272	0.62	0.81	29	empty
4	211	0.54	0.78	38	empty
5	167	0.52	0.79	34	SO4

Interfaces

11 interfaces between chains.

A–B · 2212 Å² buried · 41 hydrogen bonds · protein-protein
D–C · 2202 Å² buried · 42 hydrogen bonds · protein-protein
F–E · 2196 Å² buried · 38 hydrogen bonds · protein-protein
H–G · 2115 Å² buried · 38 hydrogen bonds · protein-protein
H–B · 830 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4KHB · Structure of the Spt16D Pob3N heterodimer · 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 G0SDN1
Every structure of UniProt G0SHK5
Elsewhere: RCSB PDB 4KHB · PDBe 4KHB · UniProt G0SDN1 · UniProt G0SHK5

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