Research workbench
The metal-free form of crystal structure of E.COLI exoi-ssdna complex
Analyse The metal-free form of crystal structure of E.COLI exoi-ssdna complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HCB
- Type
- protein + DNA
- Length
- 946 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease I; DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
- EC
- 3.1.11.1
- UniProt
- P04995
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 462 | 51% helix, 15% strand | P04995 |
| B | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 461 | 51% helix, 15% strand | P04995 |
| C | DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 12 | — | — |
| D | DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 11 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.83 | 0.85 | 125 | SO4 |
| 2 | 1012 | 0.83 | 0.84 | 113 | SO4 |
| 3 | 478 | 0.71 | 0.81 | 45 | empty |
| 4 | 71 | 0.51 | 0.85 | 28 | empty |
| 5 | 125 | 0.49 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1426 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–D · 1338 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 1184 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 247 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 245 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 4HCB · The metal-free form of crystal structure of E.coli ExoI-ssDNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- P04995 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease I (P04995) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P04995
- Elsewhere: RCSB PDB 4HCB · PDBe 4HCB · UniProt P04995
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