MolNFT v1 · #47998 · protein + DNA

DNA polymerase lambda in complex with DNA and dctp

2PFP · Template: “DNA polymerase lambda in complex with DNA and dctp”. X-ray diffraction, 3 ligands (DCP, NA, MG), 4 pockets (best druggability 0.67). MolNFT v1 #47998 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PFP
Type: protein + DNA
Length: 347 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Template; Primer; Downstream primer; DNA polymerase lambda
EC: 2.7.7.7, 4.2.99.-
UniProt: Q9UGP5
Ligands: DCP, NA, MG
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	Template	dna	11	—	—
P	Primer	dna	6	—	—
D	Downstream primer	dna	4	—	—
A	DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-)	protein	326	48% helix, 14% strand	Q9UGP5

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains T, P, A
NA · Sodium ion · metal · 5 copies · chains D, A, P, T
MG · Magnesium ion · metal · chains A

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

Pockets

4 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	798	0.67	0.75	55	MG, DCP
2	100	0.57	0.85	28	empty
3	130	0.53	0.82	21	empty
4	269	0.48	0.74	32	empty

Interfaces

5 interfaces between chains.

T–A · 963 Å² buried · 20 hydrogen bonds · protein-nucleic
D–A · 390 Å² buried · 13 hydrogen bonds · protein-nucleic
P–A · 384 Å² buried · 14 hydrogen bonds · protein-nucleic
T–P · 285 Å² buried · 22 hydrogen bonds · nucleic-nucleic
T–D · 190 Å² buried · 19 hydrogen bonds · nucleic-nucleic

Compared structures

2PFP · DNA Polymerase lambda in complex with DNA and dCTP · the same entry in another collection · chain T against T, TM-score 1.00
Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · 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 Q9UGP5
Elsewhere: RCSB PDB 2PFP · PDBe 2PFP · UniProt Q9UGP5

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