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Plla lectin, fluorophore carbohydrate complex

Analyse Plla lectin, fluorophore carbohydrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OFI
Type: protein
Length: 968 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Piia
UniProt: Q7N561
Ligands: 9TQ, CA
Pockets: 10 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A, B, D, E, F, G, H	Piia	protein	121	2% helix, 51% strand	Q7N561

Ligands and binding sites

9TQ · 5-[2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethylcarbamothioylamino]-2-(6-oxidanyl-3-oxidanylidene-4,9-dihydroxanthen-9-yl)benzoic acid · ligand · 4 copies · chains C, A, B, D
CA · Calcium ion · metal · 8 copies · chains C, A, B, D, E, F, G, H

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

Pockets

10 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	651	0.67	0.76	63	empty
2	435	0.59	0.75	41	empty
3	250	0.55	0.77	27	empty
4	60	0.37	0.79	15	empty
5	110	0.33	0.72	30	empty

Interfaces

13 interfaces between chains.

F–H · 1056 Å² buried · 18 hydrogen bonds · protein-protein
E–G · 1054 Å² buried · 17 hydrogen bonds · protein-protein
C–B · 1049 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 1046 Å² buried · 16 hydrogen bonds · protein-protein
C–E · 765 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5OFI · PllA lectin, Fluorophore carbohydrate complex · the same entry in another collection · chain H against H, TM-score 1.00
Q7N561 · AlphaFold monomer V2.0 prediction for lectin a (Q7N561) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q7N561
Elsewhere: RCSB PDB 5OFI · PDBe 5OFI · UniProt Q7N561

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