MolNFT v1 · #179697 · protein

Structure of STU2 bound to dwarf NDC80C

7KDF · NDC80 isoform 1,NDC80 isoform 1: “Structure of STU2 bound to dwarf NDC80C”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.57). MolNFT v1 #179697 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KDF
Type: protein
Length: 713 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NDC80 isoform 1,NDC80 isoform 1; NUF2 isoform 1,NUF2 isoform 1; SPC24; SPC25 isoform…
UniProt: A0A6A5Q2M2, A0A6A5Q3C2, A0A6A5PX14, A0A6A5PTU3
Ligands: SO4
Pockets: 7 · best druggability 0.57

Structure

x-ray diffraction · 5 distinct chains · 65% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NDC80 isoform 1,NDC80 isoform 1	protein	270	74% helix, 0% strand	A0A6A5Q2M2
B	NUF2 isoform 1,NUF2 isoform 1	protein	207	70% helix, 0% strand	A0A6A5Q3C2
C	SPC24	protein	95	51% helix, 8% strand	—
D	SPC25 isoform 1,SPC25 isoform 1	protein	113	50% helix, 17% strand	A0A6A5PX14
E	STU2	protein	28	61% helix, 0% strand	A0A6A5PTU3

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, E

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

Pockets

7 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	240	0.57	0.78	28	empty
2	85	0.55	0.85	19	empty
3	103	0.39	0.76	24	empty
4	72	0.36	0.77	12	empty
5	93	0.36	0.74	19	empty

Interfaces

8 interfaces between chains.

A–B · 3403 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1190 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 1067 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 983 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 796 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (engineered).

Compared structures

7KDF · Structure of Stu2 Bound to dwarf Ndc80c · 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 A0A6A5Q2M2
Every structure of UniProt A0A6A5Q3C2
Every structure of UniProt A0A6A5PX14
Every structure of UniProt A0A6A5PTU3
Elsewhere: RCSB PDB 7KDF · PDBe 7KDF · UniProt A0A6A5Q2M2 · UniProt A0A6A5Q3C2 · UniProt A0A6A5PX14 · UniProt A0A6A5PTU3

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