MolNFT v1 · #91008 · protein

Mspji restriction endonuclease - P31 form

4F0P: “Mspji restriction endonuclease - P31 form”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.88). MolNFT v1 #91008 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4F0P
Type: protein
Length: 1,803 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Restriction endonuclease
UniProt: A3PUQ5
Ligands: MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Restriction endonuclease	protein	450	32% helix, 27% strand	A3PUQ5
B, D	Restriction endonuclease	protein	452	31% helix, 26% strand	A3PUQ5
C	Restriction endonuclease	protein	449	30% helix, 26% strand	A3PUQ5

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	673	0.88	0.92	105	empty
2	594	0.87	0.93	84	empty
3	745	0.87	0.91	99	empty
4	294	0.78	0.90	50	empty
5	559	0.71	0.80	53	empty

Interfaces

6 interfaces between chains.

A–B · 4089 Å² buried · 59 hydrogen bonds · protein-protein
C–D · 1653 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1167 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 1106 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 831 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4F0P · MspJI Restriction Endonuclease - P31 Form · 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 A3PUQ5
Elsewhere: RCSB PDB 4F0P · PDBe 4F0P · UniProt A3PUQ5

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