MolNFT v1 · #102233 · protein

Crystal structure of syg-2 D3-D4

4OFP · Protein syg-2: “Crystal structure of syg-2 D3-D4”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.79). MolNFT v1 #102233 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OFP
Type: protein
Length: 781 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein syg-2
UniProt: Q9U3P2
Ligands: NAG
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Protein syg-2	protein	197	0% helix, 57% strand	Q9U3P2
B	Protein syg-2	protein	194	0% helix, 58% strand	Q9U3P2
C	Protein syg-2	protein	193	0% helix, 55% strand	Q9U3P2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, D, B, C

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	731	0.79	0.84	72	empty
2	772	0.79	0.83	76	NAG
3	275	0.61	0.80	32	empty
4	252	0.60	0.80	34	empty
5	50	0.34	0.79	19	empty

Interfaces

6 interfaces between chains.

A–D · 1901 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 1538 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1363 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 558 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 545 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

4OFP · Crystal Structure of SYG-2 D3-D4 · the same entry in another collection · chain A against A, TM-score 1.00
Q9U3P2 · AlphaFold monomer V2.0 prediction for synaptogenesis protein syg-2 (Q9U3P2) · a predicted model of the same protein · chain B against A, TM-score 0.88

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 Q9U3P2
Elsewhere: RCSB PDB 4OFP · PDBe 4OFP · UniProt Q9U3P2

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