MolNFT v1 · #55575 · protein

Long wavelength S-sad structure of FAM3B pander

2YOP · Protein FAM3B: “Long wavelength S-sad structure of FAM3B pander”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1 #55575 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YOP
Type: protein
Length: 538 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein FAM3B
UniProt: Q9D309
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein FAM3B	protein	177	12% helix, 34% strand	Q9D309
B	Protein FAM3B	protein	180	14% helix, 34% strand	Q9D309
C	Protein FAM3B	protein	181	14% helix, 34% strand	Q9D309

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

4 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	349	0.64	0.79	34	empty
2	128	0.42	0.76	21	empty
3	52	0.40	0.81	13	GOL
4	78	0.36	0.76	18	empty

Interfaces

2 interfaces between chains.

A–C · 778 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 367 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

2YOP · Long wavelength S-SAD structure of FAM3B PANDER · the same entry in another collection · chain A against A, TM-score 1.00
Q9D309 · AlphaFold monomer V2.0 prediction for protein FAM3B (Q9D309) · 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 Q9D309
Elsewhere: RCSB PDB 2YOP · PDBe 2YOP · UniProt Q9D309

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