MolNFT v1 · #89771 · protein

X-ray crystal structure of a hypothetical agmatinase from burkholderia thailandensis

4DZ4: “X-ray crystal structure of a hypothetical agmatinase from burkholderia thailandensis”. X-ray diffraction, 2 ligands (MN, UNK), 19 pockets (best druggability 0.84). MolNFT v1 #89771 on GenesisL1: 3D structure, binding sites and…

PDB: 4DZ4
Type: protein
Length: 1,900 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agmatinase
EC: 3.5.3.11
UniProt: Q2T3W4
Ligands: MN, UNK
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Agmatinase (EC 3.5.3.11)	protein	313	38% helix, 17% strand	Q2T3W4
B	Agmatinase (EC 3.5.3.11)	protein	323	37% helix, 17% strand	Q2T3W4
C, F	Agmatinase (EC 3.5.3.11)	protein	315	39% helix, 17% strand	Q2T3W4
D	Agmatinase (EC 3.5.3.11)	protein	317	38% helix, 18% strand	Q2T3W4
E	Agmatinase (EC 3.5.3.11)	protein	317	38% helix, 17% strand	Q2T3W4

Ligands and binding sites

MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
UNK · Unknown · ion · 14 copies · chains A, B, C, D, E, F
EDO · 1,2-ethanediol · additive · 47 copies · chains A, C, B, D, E, F

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.84	0.91	57	EDO
2	455	0.83	0.90	62	EDO
3	491	0.83	0.89	55	EDO
4	1066	0.78	0.80	139	EDO, UNK
5	694	0.72	0.79	80	EDO

Interfaces

12 interfaces between chains.

A–B · 1185 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 1160 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 1148 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 1023 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 1021 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4DZ4 · X-ray crystal structure of a hypothetical Agmatinase from Burkholderia thailandensis · 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 Q2T3W4
Elsewhere: RCSB PDB 4DZ4 · PDBe 4DZ4 · UniProt Q2T3W4

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