MolNFT v1 · #34444 · protein

Crystal structure of ST0656, a function unknown protein from sulfolobus tokodaii

2DGD · 223AA long hypothetical arylmalonate decarboxylase: “Crystal structure of ST0656, a function unknown protein from sulfolobus tokodaii”. X-ray diffraction, 10 pockets (best druggability 0.69). MolNFT v1 #34444 on GenesisL1: 3D…

PDB: 2DGD
Type: protein
Length: 888 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 223AA long hypothetical arylmalonate decarboxylase
EC: 4.1.1.76
Pockets: 10 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	223AA long hypothetical arylmalonate decarboxylase (EC 4.1.1.76)	protein	222	42% helix, 18% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	778	0.69	0.76	90	GOL
2	241	0.66	0.83	23	empty
3	242	0.65	0.83	26	empty
4	232	0.65	0.83	27	empty
5	265	0.65	0.82	27	empty

Interfaces

5 interfaces between chains.

C–D · 1296 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1280 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 473 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 466 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

2DGD · Crystal structure of ST0656, a function unknown protein from Sulfolobus tokodaii · the same entry in another collection · 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
Elsewhere: RCSB PDB 2DGD · PDBe 2DGD

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