MolNFT v1 · #62057 · protein + DNA

Q138F hincii bound to noncognate DNA (gtgcac) and CA2+

3E45 · Type-2 restriction enzyme hindii: “Q138F hincii bound to noncognate DNA (gtgcac) and CA2+”. X-ray diffraction, 2 ligands (CA, NA), 10 pockets (best druggability 0.68). MolNFT v1 #62057 on GenesisL1: 3D structure, binding sites and…

PDB: 3E45
Type: protein + DNA
Length: 523 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type-2 restriction enzyme hindii; 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DGP*DCP*DAP*DCP*DCP*DGP*DG…
EC: 3.1.21.4
UniProt: P44413
Ligands: CA, NA
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type-2 restriction enzyme hindii (EC 3.1.21.4)	protein	246	44% helix, 22% strand	P44413
B	Type-2 restriction enzyme hindii (EC 3.1.21.4)	protein	249	41% helix, 23% strand	P44413
E, F	5'-D(DGPDCPDCPDGPDGPDTPDGPDCPDAPDCPDCPDGPDGPD C)-3'	dna	14	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, F, B, E
NA · Sodium ion · metal · chains A, F

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	385	0.68	0.81	27	empty
2	400	0.67	0.80	29	empty
3	350	0.62	0.78	47	empty
4	52	0.60	0.92	17	empty
5	159	0.47	0.77	29	empty

Interfaces

6 interfaces between chains.

A–B · 1293 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 962 Å² buried · 21 hydrogen bonds · protein-nucleic
A–F · 909 Å² buried · 21 hydrogen bonds · protein-nucleic
B–F · 683 Å² buried · 10 hydrogen bonds · protein-nucleic
E–F · 653 Å² buried · 65 hydrogen bonds · nucleic-nucleic

Compared structures

3E45 · Q138F HincII bound to Noncognate DNA (GTGCAC) and Ca2+ · the same entry in another collection · chain A against A, TM-score 1.00
P44413 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme hindii (P44413) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P44413
Elsewhere: RCSB PDB 3E45 · PDBe 3E45 · UniProt P44413

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