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Crystal structure of the nanog homeodomain

Analyse Crystal structure of the nanog homeodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VI6
Type: protein
Length: 437 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homeobox protein nanog
UniProt: Q80Z64
Pockets: 9 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F, G	Homeobox protein nanog	protein	55	73% helix, 0% strand	Q80Z64
B, E, H	Homeobox protein nanog	protein	54	72% helix, 0% strand	Q80Z64

Pockets

9 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	50	0.59	0.91	13	empty
2	77	0.56	0.86	18	empty
3	166	0.56	0.81	38	empty
4	64	0.52	0.87	16	empty
5	57	0.52	0.87	19	empty

Interfaces

12 interfaces between chains.

C–G · 583 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 554 Å² buried · 3 hydrogen bonds · protein-protein
C–H · 418 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 392 Å² buried · 2 hydrogen bonds · protein-protein
A–G · 348 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2VI6 · Crystal Structure of the Nanog Homeodomain · the same entry in another collection · chain H against H, TM-score 1.00
Q80Z64 · AlphaFold monomer V2.0 prediction for homeobox protein nanog (Q80Z64) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 Q80Z64
Elsewhere: RCSB PDB 2VI6 · PDBe 2VI6 · UniProt Q80Z64

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