MolNFT v1 · #142464 · protein

Crystal structure of dddk mutant Y122A

6A55 · Novel protein with potential cupin domain: “Crystal structure of dddk mutant Y122A”. X-ray diffraction, 2 ligands (DQY, MN), 3 pockets (best druggability 0.64). MolNFT v1 #142464 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6A55
Type: protein
Length: 250 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Novel protein with potential cupin domain
UniProt: Q4FNM4
Ligands: DQY, MN
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Novel protein with potential cupin domain	protein	125	6% helix, 49% strand	Q4FNM4

Ligands and binding sites

DQY · 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.64	0.90	18	DQY
2	98	0.63	0.88	19	DQY
3	136	0.46	0.77	24	empty

Interfaces

1 interface between chains.

A–B · 1496 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6A55 · Crystal structure of DddK mutant Y122A · 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 Q4FNM4
Elsewhere: RCSB PDB 6A55 · PDBe 6A55 · UniProt Q4FNM4

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