Research workbench

E. COLI guanine deaminase

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

PDB: 6OHC
Type: protein
Length: 1,710 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine deaminase
EC: 3.5.4.3
UniProt: P76641
Ligands: ZN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine deaminase (EC 3.5.4.3)	protein	428	43% helix, 24% strand	P76641
B	Guanine deaminase (EC 3.5.4.3)	protein	430	43% helix, 23% strand	P76641
C	Guanine deaminase (EC 3.5.4.3)	protein	425	42% helix, 24% strand	P76641
D	Guanine deaminase (EC 3.5.4.3)	protein	427	43% helix, 24% strand	P76641

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	439	0.85	0.93	74	empty
2	292	0.85	0.96	52	empty
3	1083	0.84	0.85	102	empty
4	497	0.83	0.90	49	empty
5	409	0.82	0.90	48	empty

Interfaces

6 interfaces between chains.

A–B · 1793 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1600 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 830 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 810 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 654 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6OHC · E. coli Guanine Deaminase · the same entry in another collection · chain D against D, TM-score 1.00
P76641 · AlphaFold monomer V2.0 prediction for guanine deaminase (P76641) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P76641
Elsewhere: RCSB PDB 6OHC · PDBe 6OHC · UniProt P76641

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