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N-terminal domain of vdup-1

Analyse N-terminal domain of vdup-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GEJ
Type: protein
Length: 1,361 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioredoxin-interacting protein
UniProt: Q9H3M7
Ligands: CA
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 6 distinct chains · 0% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thioredoxin-interacting protein	protein	134	0% helix, 62% strand	Q9H3M7
B, C, F, G	Thioredoxin-interacting protein	protein	136	0% helix, 60% strand	Q9H3M7
D	Thioredoxin-interacting protein	protein	131	0% helix, 62% strand	Q9H3M7
E, I	Thioredoxin-interacting protein	protein	142	0% helix, 54% strand	Q9H3M7
H	Thioredoxin-interacting protein	protein	139	0% helix, 58% strand	Q9H3M7
J	Thioredoxin-interacting protein	protein	129	0% helix, 63% strand	Q9H3M7

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A, F, C, J, B, D, E, H, I

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	811	0.79	0.82	80	CA
2	958	0.73	0.77	77	empty
3	994	0.73	0.76	74	CA
4	793	0.72	0.78	66	CA
5	396	0.60	0.76	33	empty

Interfaces

23 interfaces between chains.

E–H · 887 Å² buried · 22 hydrogen bonds · protein-protein
B–E · 530 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 510 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 489 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 442 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4GEJ · N-terminal domain of VDUP-1 · the same entry in another collection · chain J against J, TM-score 1.00
Q9H3M7 · AlphaFold monomer V2.0 prediction for thioredoxin-interacting protein (Q9H3M7) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q9H3M7
Elsewhere: RCSB PDB 4GEJ · PDBe 4GEJ · UniProt Q9H3M7

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