MolNFT v1 · #37971 · protein + DNA

Hincii bound to cognate DNA gttaac

2GIE · 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3': “Hincii bound to cognate DNA gttaac”. X-ray diffraction, 1 ligand (NA), 13 pockets (best druggability 0.80). MolNFT v1 #37971 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2GIE
Type: protein + DNA
Length: 1,078 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*G)-3'; Type II restriction enzyme hincii
EC: 3.1.21.4
UniProt: P44413
Ligands: NA
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F, G, H	5'-D(GPCPCPGPGPTPTPAPAPCPCPGP*G)-3'	dna	13	—	—
A, C	Type II restriction enzyme hincii (EC 3.1.21.4)	protein	257	44% helix, 22% strand	P44413
B, D	Type II restriction enzyme hincii (EC 3.1.21.4)	protein	256	41% helix, 23% strand	P44413

Ligands and binding sites

NA · Sodium ion · metal · chains E, B

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

Pockets

13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	927	0.80	0.82	75	empty
2	174	0.71	0.89	27	empty
3	727	0.70	0.77	55	empty
4	321	0.70	0.84	26	empty
5	319	0.69	0.83	24	empty

Interfaces

17 interfaces between chains.

A–B · 1786 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1677 Å² buried · 9 hydrogen bonds · protein-protein
E–B · 1017 Å² buried · 25 hydrogen bonds · protein-nucleic
G–D · 1009 Å² buried · 27 hydrogen bonds · protein-nucleic
H–C · 1000 Å² buried · 27 hydrogen bonds · protein-nucleic

Compared structures

2GIE · HincII bound to cognate DNA GTTAAC · the same entry in another collection · chain D against D, 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 2GIE · PDBe 2GIE · UniProt P44413

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