CBE Database Visualizer

Select Ligand, Chain or interface (right frame) to visualize contacts of 4y3k

(Residues within 4 Angstroms of the ligand are orange)


Visualisation option: mouse right button

Entities Contact Visualizer for 4y3k

Structure of Vaspin mutant E379S
(X-RAY DIFFRACTION)



Contacts (< 4A) Between Entities (2 Chain(s) & 12 Ligand(s)) :

All Entities CHAIN_A_1 CHAIN_B_2
EDO_A_4 EDO_A_4/CHAIN_A_1 No contact
EDO_A_5 EDO_A_5/CHAIN_A_1 No contact
EDO_A_6 EDO_A_6/CHAIN_A_1 No contact
EDO_A_7 EDO_A_7/CHAIN_A_1 No contact
EDO_A_8 EDO_A_8/CHAIN_A_1 No contact
EDO_B_11 No contact EDO_B_11/CHAIN_B_2
EDO_B_14 EDO_B_14/CHAIN_A_1 EDO_B_14/CHAIN_B_2
SO4_A_10 SO4_A_10/CHAIN_A_1 SO4_A_10/CHAIN_B_2
SO4_A_3 SO4_A_3/CHAIN_A_1 No contact
SO4_A_9 SO4_A_9/CHAIN_A_1 No contact
SO4_B_12 No contact SO4_B_12/CHAIN_B_2
SO4_B_13 No contact SO4_B_13/CHAIN_B_2



Entities Features:

TypeWeightLengthInfo
CHAIN_A_1 polymer 47551.828 414 Serpin A12
CHAIN_B_2 polymer 47551.828 414 Serpin A12
EDO_A_4 non-polymer 62.068 . 1,2-ETHANEDIOL
EDO_A_5 non-polymer 62.068 . 1,2-ETHANEDIOL
EDO_A_6 non-polymer 62.068 . 1,2-ETHANEDIOL
EDO_A_7 non-polymer 62.068 . 1,2-ETHANEDIOL
EDO_A_8 non-polymer 62.068 . 1,2-ETHANEDIOL
EDO_B_11 non-polymer 62.068 . 1,2-ETHANEDIOL
EDO_B_14 non-polymer 62.068 . 1,2-ETHANEDIOL
SO4_A_10 non-polymer 96.063 . SULFATE ION
SO4_A_3 non-polymer 96.063 . SULFATE ION
SO4_A_9 non-polymer 96.063 . SULFATE ION
SO4_B_12 non-polymer 96.063 . SULFATE ION
SO4_B_13 non-polymer 96.063 . SULFATE ION


Additional CBE information:

The CBE (Contacts Between Entities) database is built from the mmCIF database.
All the molecules (entities) were extracted of the structure.
For each main chain (protein chain), amino acid in contact with ligand(s) have been obtained.
The CBE is accessible from the PDB entries.
The ligand code is :XXX_Y_Z were:
XXX = molecule short name
Y = Chain in pdb file
Z = Entity Number

[4y3k.cbe]
[4y3k.fasta)]
[4y3k.pdb)]