Entry: NAFlex_1kx5
Nucleic Sequence:
| Sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| Rev. Sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| Type | DNA |
| SubType | B |
| Chains | duplex |
| Pdb | 1KX5 |
| Ligands | No |
MD Simulation >> (Click to expand/shrink)
| Force Field | parmBSC1 |
| Simulated Time | 500 ns |
| Time Step | 10 ps |
| Parts | DNA+protein+ions |
| Temperature | 298K |
| Water Model | TIP3P |
| Additional Solvent | No |
| Counter Ions | Na+ Cl- Mn++ |
| Ionic Concentration | 0.15M |
| Additional Ions | No |
| Additional Molecules | No |
| Ions Parameters | Dang |
| RMSd | 2.432 (0.210) Å  |
| RMSf |  |
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
(Click to see full UMM)
| AdditionalIons | No |
| AdditionalMolecules | No |
| AdditionalSolvent | No |
| Author | F.B. |
| Chains | duplex |
| Comments | - |
| CounterIons | Na+ Cl- Mn++ |
| Format | mdcrd |
| FrameStep | 10 ps |
| Frames | 50000 |
| IonicConcentration | 0.15M |
| IonsParameters | Dang |
| Ligands | No |
| NucType | DNA |
| PDB | 1kx5 |
| Parts | DNA+protein+ions |
| RMSd_avg | 2.432 |
| RMSd_stdev | 0.210 |
| Rgyr_avg | 45.124 |
| Rgyr_stdev | 0.650 |
| SASA_avg | 50308.736 |
| SASA_stdev | 731.131 |
| SubType | B |
| Temperature | 298K |
| Topology | f1kx5_nowat.prmtop |
| Trajectory | f1kx5_1-1000.mdcrd |
| Water | TIP3P |
| _id | NAFlex_1kx5 |
| altPDB | 1KX5 2PYO 3B6F 3B6G 3LJA 3MGP 3MGQ 3MGR 3MGS |
| authors | Ivan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco |
| dataset | Array |
| date | 0.00000000 1429920000 |
| description | DNA-B Duplex Complex ParmBSC1 TIP3P AddedSalt Protein-nuc Nucleosome |
| forceField | parmBSC1 |
| ionsModel | - |
| moleculeType | Prot-Dna |
| rev_sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| saltConcentration | - |
| sequence | ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT |
| soluteAtoms | 21822 |
| soluteCharge | -220 |
| soluteResidues | 1058 |
| solventAtoms | - |
| solventResidues | - |
| time | 500 |
| totalAtoms | 21822 |
| totalCharge | -220 |
| totalIons | - |
| totalResidues | 1058 |
