MolNFT v1 · #126290 · protein

Structure of mitat 1.1

5LY9 · Variant surface glycoprotein mitat 1.1: “Structure of mitat 1.1”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.64). MolNFT v1 #126290 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LY9
Type: protein
Length: 732 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Variant surface glycoprotein mitat 1.1
UniProt: P26331
Ligands: NAG, MAN, BMA
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Variant surface glycoprotein mitat 1.1	protein	368	52% helix, 7% strand	P26331
B	Variant surface glycoprotein mitat 1.1	protein	364	52% helix, 7% strand	P26331

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.64	0.89	25	empty
2	228	0.52	0.77	40	GOL
3	203	0.50	0.76	34	GOL
4	145	0.46	0.77	31	NAG, GOL
5	144	0.44	0.76	27	NAG, GOL

Interfaces

1 interface between chains.

A–B · 4307 Å² buried · 66 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5LY9 · Structure of MITat 1.1 · the same entry in another collection · chain A against A, TM-score 1.00
P26331 · AlphaFold monomer V2.0 prediction for variant surface glycoprotein mitat 1.1 (P26331) · a predicted model of the same protein · 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 P26331
Elsewhere: RCSB PDB 5LY9 · PDBe 5LY9 · UniProt P26331

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