MolNFT v1 · #37976 · protein + DNA

Q138F hincii bound to cognate DNA gttaac and CA2+

2GIJ · 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*GP*C)-3': “Q138F hincii bound to cognate DNA gttaac and CA2+”. X-ray diffraction, 2 ligands (CA, NA), 8 pockets (best druggability 0.70). MolNFT v1 #37976 on GenesisL1: 3D structure, binding…

PDB: 2GIJ
Type: protein + DNA
Length: 509 residues
Chains: 4
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*GP*C)-3'; Type II restriction enzyme hincii
EC: 3.1.21.4
UniProt: P17743
Ligands: CA, NA
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F	5'-D(GPCPCPGPGPTPTPAPAPCPCPGPGPC)-3'	dna	14	—	—
A	Type II restriction enzyme hincii (EC 3.1.21.4)	protein	245	45% helix, 23% strand	P17743
B	Type II restriction enzyme hincii (EC 3.1.21.4)	protein	236	44% helix, 21% strand	P17743

Ligands and binding sites

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

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	505	0.70	0.80	41	empty
2	421	0.69	0.81	26	empty
3	244	0.53	0.76	33	empty
4	88	0.45	0.81	18	CA
5	153	0.44	0.75	18	empty

Interfaces

6 interfaces between chains.

A–B · 1273 Å² buried · 5 hydrogen bonds · protein-protein
F–A · 882 Å² buried · 25 hydrogen bonds · protein-nucleic
E–B · 801 Å² buried · 17 hydrogen bonds · protein-nucleic
E–F · 638 Å² buried · 45 hydrogen bonds · nucleic-nucleic
E–A · 575 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

2GIJ · Q138F HincII bound to cognate DNA GTTAAC and Ca2+ · the same entry in another collection · chain E against E, TM-score 1.00
P17743 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme hincii (P17743) · a predicted model of the same protein · chain B 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 P17743
Elsewhere: RCSB PDB 2GIJ · PDBe 2GIJ · UniProt P17743

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