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Crystal structure of blasticidin S deaminase (bsd) R90K mutant

Analyse Crystal structure of blasticidin S deaminase (bsd) R90K mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z3J
Type: protein
Length: 504 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blasticidin-S deaminase
EC: 3.5.4.23
UniProt: P0C2P0
Ligands: ZN, CL
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Blasticidin-S deaminase (EC 3.5.4.23)	protein	127	31% helix, 26% strand	P0C2P0
B	Blasticidin-S deaminase (EC 3.5.4.23)	protein	128	30% helix, 26% strand	P0C2P0
C	Blasticidin-S deaminase (EC 3.5.4.23)	protein	125	32% helix, 26% strand	P0C2P0
D	Blasticidin-S deaminase (EC 3.5.4.23)	protein	124	32% helix, 27% strand	P0C2P0

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
CL · Chloride ion · ion · chains A, B, C, D
CAC · Cacodylate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	165	0.60	0.83	27	CAC
2	155	0.59	0.83	31	CAC
3	96	0.55	0.85	22	CAC
4	128	0.55	0.82	26	CAC
5	55	0.32	0.77	15	empty

Interfaces

6 interfaces between chains.

B–C · 1226 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 1147 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 800 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 675 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 361 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2Z3J · Crystal structure of blasticidin S deaminase (BSD) R90K mutant · the same entry in another collection · chain D against D, TM-score 1.00
P0C2P0 · AlphaFold monomer V2.0 prediction for blasticidin-S deaminase (P0C2P0) · a predicted model of the same protein · chain D 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 P0C2P0
Elsewhere: RCSB PDB 2Z3J · PDBe 2Z3J · UniProt P0C2P0

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