Research workbench
Structural basis of human clamp sliding on DNA
Analyse Structural basis of human clamp sliding on DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GIS
- Type
- protein + DNA
- Length
- 764 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3'); DNA…
- UniProt
- P12004
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 248 | 20% helix, 47% strand | P12004 |
| B | Proliferating cell nuclear antigen | protein | 250 | 20% helix, 47% strand | P12004 |
| C | Proliferating cell nuclear antigen | protein | 246 | 20% helix, 47% strand | P12004 |
| D | DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3') | dna | 10 | — | — |
| E | DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3') | dna | 10 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.75 | 0.78 | 71 | empty |
| 2 | 58 | 0.28 | 0.74 | 21 | empty |
| 3 | 54 | 0.25 | 0.73 | 16 | empty |
Interfaces
7 interfaces between chains.
- B–C · 648 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 632 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 454 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–D · 210 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GIS · Structural basis of human clamp sliding on DNA · the same entry in another collection · chain A against A, 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 P12004
- Elsewhere: RCSB PDB 6GIS · PDBe 6GIS · UniProt P12004
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