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3.0 a X-ray structure of putative oligoendopeptidase F: crystals grown by vapor diffusion technique

Analyse 3.0 a X-ray structure of putative oligoendopeptidase F: crystals grown by vapor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2H1N
Type: protein
Length: 1,132 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligoendopeptidase F
EC: 3.4.24.-
Ligands: UNL, ZN
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Oligoendopeptidase F (EC 3.4.24.-)	protein	566	69% helix, 4% strand	—

Ligands and binding sites

UNL · Unknown ligand · ligand · 6 copies · chains A, B
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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	494	0.82	0.89	67	UNL
2	481	0.82	0.89	61	UNL
3	348	0.78	0.88	51	empty
4	211	0.73	0.89	32	UNL
5	68	0.56	0.88	11	empty

Modifications

Observed in the structure: 28 modified (engineered).

Compared structures

2H1N · 3.0 A X-ray structure of putative oligoendopeptidase F: crystals grown by vapor diffusion… · 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
Elsewhere: RCSB PDB 2H1N · PDBe 2H1N

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