MolNFT v1 · #115924 · protein + DNA

TN3 resolvase - site III complex crystal form I

5CY1 · Transposon TN3 resolvase: “TN3 resolvase - site III complex crystal form I”. X-ray diffraction, 6 pockets (best druggability 0.63). MolNFT v1 #115924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CY1
Type: protein + DNA
Length: 423 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transposon TN3 resolvase; DNA (30-mer)
UniProt: P0ADI2
Pockets: 6 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 55% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transposon TN3 resolvase	protein	183	53% helix, 11% strand	P0ADI2
B	Transposon TN3 resolvase	protein	180	57% helix, 11% strand	P0ADI2
C	DNA (30-mer)	dna	30	—	—
D	DNA (30-mer)	dna	30	—	—

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	501	0.63	0.76	49	empty
2	96	0.58	0.87	17	empty
3	146	0.49	0.79	19	empty
4	113	0.44	0.78	21	empty
5	68	0.35	0.77	17	empty

Interfaces

6 interfaces between chains.

A–B · 1688 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1268 Å² buried · 112 hydrogen bonds · nucleic-nucleic
B–C · 913 Å² buried · 27 hydrogen bonds · protein-nucleic
B–D · 867 Å² buried · 16 hydrogen bonds · protein-nucleic
A–C · 663 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

5CY1 · Tn3 resolvase - site III complex crystal form I · the same entry in another collection · chain A against A, 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 0.66

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 5CY1 · PDBe 5CY1 · UniProt P0ADI2

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