MolNFT v1 · #122509 · protein

Structural insight into host cell surface retention of a 1.5-mda bacterial ice-binding adhesin

5IRB · Rtx-adhesin: “Structural insight into host cell surface retention of a 1.5-mda bacterial ice-binding adhesin”. X-ray diffraction, 2 ligands (CA, MG), 2 pockets (best druggability 0.54). MolNFT v1 #122509 on GenesisL1: 3D structure…

PDB: 5IRB
Type: protein
Length: 627 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rtx-adhesin
UniProt: A1YIY2
Ligands: CA, MG
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rtx-adhesin	protein	313	10% helix, 54% strand	A1YIY2
B	Rtx-adhesin	protein	314	10% helix, 55% strand	A1YIY2

Ligands and binding sites

CA · Calcium ion · metal · 17 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains B
EDO · 1,2-ethanediol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	136	0.54	0.82	27	empty
2	50	0.28	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 770 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5IRB · Structural insight into host cell surface retention of a 1.5-MDa bacterial ice-binding… · 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 A1YIY2
Elsewhere: RCSB PDB 5IRB · PDBe 5IRB · UniProt A1YIY2

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