Download MendeleyScrunching 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.
3HWT
Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched dA
- PDB DOI: https://doi.org/10.2210/pdb3HWT/pdb
- NAKB: 3HWT
- Classification: TRANSFERASE/DNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2009-06-18 Released: 2009-08-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.261
- R-Value Work: 0.228
Starting Model: experimental
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This is version 1.5 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase lambda | 335 | Homo sapiens | Mutation(s): 1 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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UGP5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3' | B [auth T] | 12 | N/A |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*CP*AP*GP*TP*AP*(2DT))-3' | C [auth P] | 6 | N/A |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| D3T Query on D3T | E [auth A] | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O13 P3 URGJWIFLBWJRMF-JGVFFNPUSA-N |  | ||
| EDO Query on EDO | H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MG Query on MG | F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | G [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.261
- R-Value Work: 0.228
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.023 | α = 90 |
| b = 68.328 | β = 90 |
| c = 137.85 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
Entry History
Deposition Data
- Released Date: 2009-08-25 Deposition Author(s): Garcia-Diaz, M., Bebenek, K., Larrea, A.A., Pedersen, L.C., Kunkel, T.A.
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: 2013-09-25
Changes: Derived calculations - Version 1.3: 2017-11-01
Changes: Refinement description - Version 1.4: 2021-10-13
Changes: Database references, Derived calculations - Version 1.5: 2023-09-06
Changes: Data collection, Refinement description
