MolNFT v1 · #27741 · protein + DNA

Crystal structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate

1XSP · 5'-D(*CP*GP*GP*CP*CP*GP*TP*AP*CP*TP*G)-3': “Crystal structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate”. X-ray diffraction, 2 ligands (PPV, NA), 4 pockets (best druggability 0.66). MolNFT v1 #27741…

PDB: 1XSP
Type: protein + DNA
Length: 349 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*GP*GP*CP*CP*GP*TP*AP*CP*TP*G)-3'; 5'-D(*CP*AP*GP*TP*AP*CP*G)-3'…
EC: 2.7.7.7
UniProt: Q9UGP5
Ligands: PPV, NA
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	5'-D(CPGPGPCPCPGPTPAPCPTP*G)-3'	dna	11	—	—
P	5'-D(CPAPGPTPAPCP*G)-3'	dna	7	—	—
D	5'-D(PGPCPCPG)-3'	dna	4	—	—
A	DNA polymerase lambda (EC 2.7.7.7)	protein	327	47% helix, 14% strand	Q9UGP5

Ligands and binding sites

PPV · Pyrophosphate · ligand · chains P, A
NA · Sodium ion · metal · 4 copies · chains D, A, P, T

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	583	0.66	0.77	40	NA, PPV
2	108	0.55	0.84	31	empty
3	136	0.52	0.81	23	empty
4	174	0.47	0.76	21	empty

Interfaces

5 interfaces between chains.

T–A · 943 Å² buried · 19 hydrogen bonds · protein-nucleic
P–A · 590 Å² buried · 19 hydrogen bonds · protein-nucleic
D–A · 393 Å² buried · 10 hydrogen bonds · protein-nucleic
T–P · 327 Å² buried · 26 hydrogen bonds · nucleic-nucleic
T–D · 186 Å² buried · 14 hydrogen bonds · nucleic-nucleic

Compared structures

1XSP · Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and… · 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 0.98

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 1XSP · PDBe 1XSP · UniProt Q9UGP5

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