MolNFT v2 · #34833 · protein

Crystal structure of mabinlin II

2DS2 · Sweet protein mabinlin-2 chain A: “Crystal structure of mabinlin II”. X-ray diffraction at 1.7, 1 pocket (best druggability 0.43). MolNFT v2 #34833 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DS2
Type: protein
Length: 189 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Source: Capparis masaikai
Molecule: Sweet protein mabinlin-2 chain A; Sweet protein mabinlin-2 chain B
UniProt: P30233
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · resolution 1.7 · 4 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sweet protein mabinlin-2 chain A	protein	26	85% helix, 0% strand	P30233
B	Sweet protein mabinlin-2 chain B	protein	67	66% helix, 0% strand	P30233
C	Sweet protein mabinlin-2 chain A	protein	28	89% helix, 0% strand	P30233
D	Sweet protein mabinlin-2 chain B	protein	68	66% helix, 0% strand	P30233

Ligands and binding sites

ACY · Acetic acid · additive · chains D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.43	0.75	28	ACY

Interfaces

4 interfaces between chains.

C–D · 1280 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1208 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 396 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 28 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2DS2 · Crystal structure of mabinlin II · the same entry in another collection · chain D against D, TM-score 1.00
P30233 · AlphaFold monomer V2.0 prediction for sweet protein mabinlin-2 (P30233) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P30233
Elsewhere: RCSB PDB 2DS2 · PDBe 2DS2 · UniProt P30233

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