MolNFT v1 · #78865 · protein

Crystal structure of NMB0315

3SLU · M23 peptidase domain protein: “Crystal structure of NMB0315”. X-ray diffraction, 1 ligand (NI), 10 pockets (best druggability 0.74). MolNFT v1 #78865 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SLU
Type: protein
Length: 709 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: M23 peptidase domain protein
UniProt: E0N688
Ligands: NI
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	M23 peptidase domain protein	protein	351	17% helix, 40% strand	E0N688
B	M23 peptidase domain protein	protein	358	14% helix, 41% strand	E0N688

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	866	0.74	0.78	116	empty
2	550	0.69	0.79	87	empty
3	132	0.56	0.83	31	empty
4	197	0.52	0.77	24	empty
5	119	0.46	0.79	28	empty

Interfaces

1 interface between chains.

A–B · 1250 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3SLU · Crystal structure of NMB0315 · 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 E0N688
Elsewhere: RCSB PDB 3SLU · PDBe 3SLU · UniProt E0N688

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