MolNFT v1 · #146531 · protein

Yeast DDI2 cyanamide hydratase

6DKA · DNA damage-inducible protein: “Yeast DDI2 cyanamide hydratase”. X-ray diffraction, 3 ligands (CNN, ZN, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #146531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DKA
Type: protein
Length: 2,063 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA damage-inducible protein
UniProt: A7A1Y4
Ligands: CNN, ZN, SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 62% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	DNA damage-inducible protein	protein	230	62% helix, 2% strand	A7A1Y4
D, G	DNA damage-inducible protein	protein	229	62% helix, 2% strand	A7A1Y4
E	DNA damage-inducible protein	protein	230	62% helix, 2% strand	A7A1Y4
F	DNA damage-inducible protein	protein	232	62% helix, 3% strand	A7A1Y4
H	DNA damage-inducible protein	protein	227	62% helix, 2% strand	A7A1Y4
I	DNA damage-inducible protein	protein	226	62% helix, 2% strand	A7A1Y4

Ligands and binding sites

CNN · Cyanamide · ligand · 7 copies · chains A, B, C, D, E, F, G
ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F, G, H, I
SO4 · Sulfate ion · ion · 26 copies · chains A, B, C, E, D, G, F, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	996	0.82	0.83	128	SO4
2	773	0.80	0.83	104	SO4
3	414	0.72	0.83	58	empty
4	263	0.69	0.85	44	SO4
5	259	0.67	0.83	44	empty

Interfaces

18 interfaces between chains.

H–I · 1504 Å² buried · 20 hydrogen bonds · protein-protein
F–G · 1435 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1412 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1395 Å² buried · 19 hydrogen bonds · protein-protein
C–E · 747 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6DKA · Yeast Ddi2 Cyanamide Hydratase · 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 A7A1Y4
Elsewhere: RCSB PDB 6DKA · PDBe 6DKA · UniProt A7A1Y4

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