MolNFT v1 · #67364 · protein

Crystal structure of peptidase M28 precursor (YP_926796.1) from shewanella amazonensis SB2B at 1.70 a resolution

3IIB: “Crystal structure of peptidase M28 precursor (YP_926796.1) from shewanella amazonensis SB2B at 1.70 a…”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.60). MolNFT v1 #67364 on GenesisL1: 3D structure, binding…

PDB: 3IIB
Type: protein
Length: 442 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidase M28
UniProt: A1S420
Ligands: ZN
Pockets: 2 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidase M28	protein	442	38% helix, 26% strand	A1S420

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
PGE · Triethylene glycol · additive · chains A

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	388	0.60	0.76	39	empty
2	50	0.39	0.81	16	empty

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

3IIB · Crystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS… · 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 A1S420
Elsewhere: RCSB PDB 3IIB · PDBe 3IIB · UniProt A1S420

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