3HX0 | pdb_00003hx0

ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.268 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Scrunching During DNA Repair Synthesis

Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Havener, J.M., Perera, L., Krahn, J.M., Pedersen, L.C., Ramsden, D.A., Kunkel, T.A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 177.77 kDa 
  • Atom Count: 11,946 
  • Modeled Residue Count: 1,401 
  • Deposited Residue Count: 1,428 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 3

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase lambdaA,
E [auth F],
I [auth K],
M [auth P]		335Homo sapiensMutation(s): 4 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5
GTEx:  ENSG00000166169 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGP5
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'B,
F [auth G],
J [auth L],
N [auth Q]		12N/A
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*CP*AP*GP*TP*AP*T)-3'C,
G [auth H],
K [auth M],
O [auth R]		6N/A
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(P*GP*CP*CP*G)-3'D,
H [auth I],
L [auth N],
P [auth S]		4N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D3T

Query on D3T


Download:Ideal Coordinates CCD File
Q [auth A],
S [auth F],
V [auth K],
Z [auth P]		2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
AA [auth P],
R [auth A],
T [auth F],
W [auth K]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
BA [auth P],
CA [auth P],
U [auth F],
X [auth K],
Y [auth K]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.268 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.179α = 90
b = 131.912β = 90
c = 280.412γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description