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Peptide-bound structure of marinomonas primoryensis peptide-binding domain

Analyse Peptide-bound structure of marinomonas primoryensis peptide-binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X5V
Type: protein
Length: 506 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antifreeze protein; Peptide
UniProt: A1YIY3
Ligands: CA
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antifreeze protein	protein	502	4% helix, 51% strand	A1YIY3
B	Peptide	protein	4	0% helix, 25% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 17 copies · chains A, B
1PE · Pentaethylene glycol · additive · 3 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.36	0.73	25	1PE
2	53	0.24	0.73	11	empty

Interfaces

1 interface between chains.

A–B · 282 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6X5V · Peptide-bound structure of Marinomonas primoryensis peptide-binding domain · 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 A1YIY3
Elsewhere: RCSB PDB 6X5V · PDBe 6X5V · UniProt A1YIY3

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