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.
3HX0
ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA
- PDB DOI: https://doi.org/10.2210/pdb3HX0/pdb
- NAKB: 3HX0
- Classification: TRANSFERASE/DNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2009-06-19 Released: 2009-08-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.268
- R-Value Work: 0.223
- R-Value Observed: 0.223
Starting Model: experimental
View more details
This is version 1.3 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 | A, E [auth F], I [auth K], M [auth P] | 335 | Homo sapiens | Mutation(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 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, F [auth G], J [auth L], N [auth Q] | 12 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*CP*AP*GP*TP*AP*T)-3' | C, G [auth H], K [auth M], O [auth R] | 6 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(P*GP*CP*CP*G)-3' | D, H [auth I], L [auth N], P [auth S] | 4 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| D3T Query on D3T | 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 | AA [auth P], R [auth A], T [auth F], W [auth K] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | 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
- R-Value Work: 0.223
- R-Value Observed: 0.223
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 124.179 | α = 90 |
| b = 131.912 | β = 90 |
| c = 280.412 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| MOLREP | phasing |
| CNS | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-08-25 Deposition Author(s): 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.
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
