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Structure of sialic acid binding protein (siap) in the presence of kdn

Analyse Structure of sialic acid binding protein (siap) in the presence of kdn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V4C
Type: protein
Length: 309 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sialic acid-binding periplasmic protein siap
UniProt: P44542
Ligands: KDN
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sialic acid-binding periplasmic protein siap	protein	309	52% helix, 19% strand	P44542

Ligands and binding sites

KDN · deamino-beta-neuraminic acid · sugar · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.80	0.94	45	KDN
2	56	0.29	0.74	13	empty

Compared structures

2V4C · Structure of sialic acid binding protein (SiaP) in the presence of KDN · the same entry in another collection · chain A against A, TM-score 1.00
P44542 · AlphaFold monomer V2.0 prediction for sialic acid-binding periplasmic protein siap… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P44542
Elsewhere: RCSB PDB 2V4C · PDBe 2V4C · UniProt P44542

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