MolNFT v2 · #219523 · protein

Urethanase umg-sp1 without inhibitor or substrate displays flexible active site loops

8S7Z: “Urethanase umg-sp1 without inhibitor or substrate displays flexible active site loops”. X-ray diffraction at 2.67, 20 pockets (best druggability 0.79). MolNFT v2 #219523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8S7Z
Type: protein
Length: 1,488 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.67
Source: metagenome
Molecule: Urethanase umg-sp1
EC: 3.5.1.75
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · resolution 2.67 · 4 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Urethanase umg-sp1 (EC 3.5.1.75)	protein	372	42% helix, 16% strand	—
B	Urethanase umg-sp1 (EC 3.5.1.75)	protein	371	41% helix, 16% strand	—
C	Urethanase umg-sp1 (EC 3.5.1.75)	protein	372	42% helix, 16% strand	—
D	Urethanase umg-sp1 (EC 3.5.1.75)	protein	373	42% helix, 17% strand	—

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1131	0.79	0.80	118	empty
2	344	0.66	0.81	32	empty
3	423	0.63	0.77	57	empty
4	231	0.56	0.78	36	empty
5	214	0.52	0.77	31	empty

Interfaces

4 interfaces between chains.

A–B · 1025 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 1012 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 245 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 40 Å² buried · 0 hydrogen bonds · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8S7Z · PDBe 8S7Z

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