MolNFT v1 · #121231 · protein + DNA

Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and metal ions

5HP4 · DNA (5'- D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*…: “Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and…”. X-ray diffraction, 3 ligands (CA, NA, K), 1 pocket (best…

PDB: 5HP4
Type: protein + DNA
Length: 289 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3'); Exodeoxyribonuclease
EC: 3.1.11.3
UniProt: P06229
Ligands: CA, NA, K
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	DNA (5'- D(GPAPTPCPTPAPTPAPTPGPCPCPAPTPCPGP*G)-3')	dna	17	—	—
A	Exodeoxyribonuclease (EC 3.1.11.3)	protein	272	60% helix, 11% strand	P06229

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains X, A
NA · Sodium ion · metal · chains X
K · Potassium ion · metal · chains X, A
GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1124	0.73	0.77	83	K, CA, GOL

Interfaces

1 interface between chains.

X–A · 1012 Å² buried · 19 hydrogen bonds · protein-nucleic

Compared structures

5HP4 · Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product… · the same entry in another collection · chain X against X, TM-score 1.00

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 P06229
Elsewhere: RCSB PDB 5HP4 · PDBe 5HP4 · UniProt P06229

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