MolNFT v1 · #140950 · protein

Crystal structure of the eal domain of mycobacterium smegmatis dcpa

5YRP · Sensory BOX/RESPONSE regulator: “Crystal structure of the eal domain of mycobacterium smegmatis dcpa”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.38). MolNFT v1 #140950 on GenesisL1: 3D structure, binding sites…

PDB: 5YRP
Type: protein
Length: 447 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sensory BOX/RESPONSE regulator
UniProt: A0QUG3
Ligands: MG
Pockets: 1 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sensory BOX/RESPONSE regulator	protein	224	39% helix, 25% strand	A0QUG3
B	Sensory BOX/RESPONSE regulator	protein	223	38% helix, 23% strand	A0QUG3

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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	109	0.38	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 894 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

5YRP · Crystal structure of the EAL domain of Mycobacterium smegmatis DcpA · 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
Every structure of UniProt A0QUG3
Elsewhere: RCSB PDB 5YRP · PDBe 5YRP · UniProt A0QUG3

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