Research workbench
POSTS3_PMAR_LIG4_WT
Analyse POSTS3_PMAR_LIG4_WT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RAU
- Type
- protein + DNA
- Length
- 474 residues
- Chains
- 3
- 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 (5'…
- UniProt
- A0A0A2ACP7
- Ligands
- AMP, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 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 (5'- D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)- 3') | dna | 21 | — | — |
| I | ATP-dependent DNA ligase | protein | 432 | 38% helix, 26% strand | A0A0A2ACP7 |
Ligands and binding sites
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 | 1062 | 0.81 | 0.82 | 68 | AMP, SO4 |
| 2 | 496 | 0.69 | 0.80 | 40 | empty |
| 3 | 318 | 0.64 | 0.81 | 39 | empty |
| 4 | 130 | 0.47 | 0.78 | 28 | empty |
| 5 | 58 | 0.33 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–I · 1330 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–I · 1172 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–C · 957 Ų buried · 93 hydrogen bonds · nucleic-nucleic
Compared structures
- 6RAU · PostS3_Pmar_lig4_WT · 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 6RAU · PDBe 6RAU · UniProt A0A0A2ACP7
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