MolNFT v1 · #139793 · protein

Crystal structure of full-length human rogdi

5XQI · Protein rogdi homolog: “Crystal structure of full-length human rogdi”. X-ray diffraction, 14 pockets (best druggability 0.65). MolNFT v1 #139793 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XQI
Type: protein
Length: 1,060 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein rogdi homolog
UniProt: Q9GZN7
Pockets: 14 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein rogdi homolog	protein	275	41% helix, 25% strand	Q9GZN7
B	Protein rogdi homolog	protein	276	41% helix, 25% strand	Q9GZN7
C	Protein rogdi homolog	protein	254	48% helix, 26% strand	Q9GZN7
D	Protein rogdi homolog	protein	255	47% helix, 24% strand	Q9GZN7

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	699	0.65	0.75	70	empty
2	328	0.59	0.77	34	empty
3	327	0.53	0.74	30	empty
4	212	0.50	0.76	27	empty
5	100	0.47	0.80	19	empty

Interfaces

5 interfaces between chains.

A–C · 815 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 782 Å² buried · 1 hydrogen bond · protein-protein
A–D · 528 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 514 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 412 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5XQI · Crystal structure of full-length human Rogdi · the same entry in another collection · chain D against D, TM-score 1.00
Q9GZN7 · AlphaFold monomer V2.0 prediction for protein rogdi homolog (Q9GZN7) · a predicted model of the same protein · chain C 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 Q9GZN7
Elsewhere: RCSB PDB 5XQI · PDBe 5XQI · UniProt Q9GZN7

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