MolNFT v1 · #115925 · protein + DNA

TN3 resolvase - site III complex crystal form II

5CY2 · Transposon TN3 resolvase: “TN3 resolvase - site III complex crystal form II”. X-ray diffraction, 12 pockets (best druggability 0.69). MolNFT v1 #115925 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CY2
Type: protein + DNA
Length: 821 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transposon TN3 resolvase; DNA (27-mer)
UniProt: P0ADI2
Pockets: 12 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 54% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transposon TN3 resolvase	protein	177	53% helix, 11% strand	P0ADI2
B, F	Transposon TN3 resolvase	protein	180	56% helix, 9% strand	P0ADI2
C, G	DNA (27-mer)	dna	27	—	—
D, H	DNA (27-mer)	dna	27	—	—
E	Transposon TN3 resolvase	protein	176	53% helix, 11% strand	P0ADI2

Pockets

12 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	54	0.69	0.96	20	empty
2	136	0.61	0.86	18	empty
3	120	0.60	0.86	17	empty
4	283	0.55	0.76	40	empty
5	152	0.49	0.78	24	empty

Interfaces

13 interfaces between chains.

A–B · 1631 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1599 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1100 Å² buried · 99 hydrogen bonds · nucleic-nucleic
G–H · 1092 Å² buried · 96 hydrogen bonds · nucleic-nucleic
B–C · 910 Å² buried · 19 hydrogen bonds · protein-nucleic

Compared structures

5CY2 · Tn3 resolvase - site III complex crystal form II · the same entry in another collection · chain H against H, TM-score 1.00
P0ADI2 · AlphaFold monomer V2.0 prediction for transposon TN3 resolvase (P0ADI2) · a predicted model of the same protein · chain A against A, TM-score 0.69

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 P0ADI2
Elsewhere: RCSB PDB 5CY2 · PDBe 5CY2 · UniProt P0ADI2

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