MolNFT v1 · #58467 · protein

Site-2 protease from methanocaldococcus jannaschii

3B4R · Putative zinc metalloprotease MJ0392: “Site-2 protease from methanocaldococcus jannaschii”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.82). MolNFT v1 #58467 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3B4R
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative zinc metalloprotease MJ0392
EC: 3.4.24.-
UniProt: Q57837
Ligands: ZN
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative zinc metalloprotease MJ0392 (EC 3.4.24.-)	protein	218	67% helix, 10% strand	Q57837
B	Putative zinc metalloprotease MJ0392 (EC 3.4.24.-)	protein	216	62% helix, 10% strand	Q57837

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	669	0.82	0.86	46	empty
2	1089	0.77	0.78	100	ZN
3	158	0.49	0.78	22	empty
4	98	0.43	0.78	20	empty
5	62	0.35	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1318 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3B4R · Site-2 Protease from Methanocaldococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
Q57837 · AlphaFold monomer V2.0 prediction for zinc metalloprotease MJ0392 (Q57837) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q57837
Elsewhere: RCSB PDB 3B4R · PDBe 3B4R · UniProt Q57837

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