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Crystal structure of xrbj

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

PDB: 6JMG
Type: protein
Length: 530 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dnaj homolog subfamily C member 27-a
UniProt: Q7ZYF1
Ligands: GTP, MG
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dnaj homolog subfamily C member 27-a	protein	267	46% helix, 18% strand	Q7ZYF1
B	Dnaj homolog subfamily C member 27-a	protein	263	45% helix, 18% strand	Q7ZYF1

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

5 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	1056	0.83	0.84	80	empty
2	276	0.62	0.80	40	GTP, MG
3	197	0.57	0.80	39	GTP, MG
4	79	0.39	0.78	16	empty
5	75	0.37	0.77	12	empty

Interfaces

1 interface between chains.

A–B · 1399 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6JMG · Crystal structure of xRbj · the same entry in another collection · chain A against A, TM-score 1.00
Q7ZYF1 · AlphaFold monomer V2.0 prediction for dnaj homolog subfamily C member 27-a (Q7ZYF1) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q7ZYF1
Elsewhere: RCSB PDB 6JMG · PDBe 6JMG · UniProt Q7ZYF1

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