MolNFT v1 · #3060 · protein

Hydrogenase maturating endopeptidase hybd from E. COLI

1CFZ · Hydrogenase 2 maturation protease: “Hydrogenase maturating endopeptidase hybd from E. COLI”. X-ray diffraction, 1 ligand (CD), 2 pockets (best druggability 0.56). MolNFT v1 #3060 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1CFZ
Type: protein
Length: 972 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydrogenase 2 maturation protease
EC: 3.4.-.-
UniProt: P37182
Ligands: CD
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Hydrogenase 2 maturation protease (EC 3.4.-.-)	protein	162	40% helix, 23% strand	P37182

Ligands and binding sites

CD · Cadmium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	426	0.56	0.73	65	empty
2	50	0.28	0.74	14	empty

Interfaces

6 interfaces between chains.

A–E · 505 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 405 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 396 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 391 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 390 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1CFZ · Hydrogenase maturating endopeptidase hybd from E. COLI · the same entry in another collection · chain C against C, TM-score 1.00
P37182 · AlphaFold monomer V2.0 prediction for hydrogenase 2 maturation protease (P37182) · a predicted model of the same protein · 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 P37182
Elsewhere: RCSB PDB 1CFZ · PDBe 1CFZ · UniProt P37182

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