Research workbench

E. COLI agmatinase

Analyse E. COLI agmatinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LBA
Type: protein
Length: 5,481 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agmatinase
EC: 3.5.3.11
UniProt: S0XV43
Ligands: MN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 8 distinct chains · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Agmatinase (EC 3.5.3.11)	protein	305	40% helix, 15% strand	S0XV43
B, K	Agmatinase (EC 3.5.3.11)	protein	310	40% helix, 15% strand	S0XV43
C, I, O	Agmatinase (EC 3.5.3.11)	protein	305	40% helix, 15% strand	S0XV43
D, H, J, N, P, Q	Agmatinase (EC 3.5.3.11)	protein	303	39% helix, 16% strand	S0XV43
E	Agmatinase (EC 3.5.3.11)	protein	309	38% helix, 16% strand	S0XV43
F, L	Agmatinase (EC 3.5.3.11)	protein	302	39% helix, 16% strand	S0XV43
M	Agmatinase (EC 3.5.3.11)	protein	304	39% helix, 16% strand	S0XV43
R	Agmatinase (EC 3.5.3.11)	protein	301	40% helix, 16% strand	S0XV43

Ligands and binding sites

MN · Manganese (II) ion · metal · 27 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, P, Q

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1093	0.87	0.89	92	empty
2	1067	0.87	0.88	103	empty
3	927	0.82	0.84	93	MN
4	425	0.82	0.90	38	empty
5	1054	0.82	0.83	94	empty

Interfaces

41 interfaces between chains.

P–Q · 1439 Å² buried · 12 hydrogen bonds · protein-protein
N–R · 1431 Å² buried · 14 hydrogen bonds · protein-protein
G–I · 1408 Å² buried · 12 hydrogen bonds · protein-protein
J–K · 1399 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 1392 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7LBA · E. coli Agmatinase · 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 S0XV43
Elsewhere: RCSB PDB 7LBA · PDBe 7LBA · UniProt S0XV43

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.