Research workbench
Pmar-LIG_PRES3-mn
Analyse Pmar-LIG_PRES3-mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RAR
- Type
- protein + DNA
- Length
- 474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)- 3'); DNA/RNA…
- UniProt
- A0A0A2ACP7
- Ligands
- AMP, MN, SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(*TP*TP*CP*CP*GP*AP*CP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)- 3') | dna | 21 | — | — |
| C | DNA/RNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC))-D(P*C)- 3') | dna | 10 | — | — |
| D | DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3') | dna | 11 | — | — |
| I | ATP-dependent DNA ligase | protein | 432 | 38% helix, 26% strand | A0A0A2ACP7 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains D, I
- MN · Manganese (II) ion · metal · chains C, D, I
- SO4 · Sulfate ion · ion · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.82 | 71 | AMP, SO4 |
| 2 | 515 | 0.70 | 0.80 | 41 | empty |
| 3 | 254 | 0.59 | 0.80 | 27 | empty |
| 4 | 145 | 0.45 | 0.77 | 15 | empty |
| 5 | 107 | 0.43 | 0.78 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–I · 1370 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–I · 625 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–I · 625 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 540 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–C · 456 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 6RAR · Pmar-Lig_PreS3-Mn · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A0A2ACP7
- Elsewhere: RCSB PDB 6RAR · PDBe 6RAR · UniProt A0A0A2ACP7
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