MolNFT v1 · #93764 · protein + DNA
The zinc ion bound form of crystal structure of E.COLI exoi-ssdna complex
4HCC · Exodeoxyribonuclease I: “The zinc ion bound form of crystal structure of E.COLI exoi-ssdna complex”. X-ray diffraction, 3 ligands (ZN, SO4, PO4), 14 pockets (best druggability 0.77). MolNFT v1 #93764 on GenesisL1: 3D structure…
- PDB
- 4HCC
- Type
- protein + DNA
- Length
- 948 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
- ZN, SO4, PO4
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 465 | 50% helix, 14% strand | P04995 |
| B | Exodeoxyribonuclease I (EC 3.1.11.1) | protein | 463 | 52% helix, 15% strand | P04995 |
| C, D | DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, C, B, D
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.77 | 0.79 | 109 | SO4 |
| 2 | 1055 | 0.75 | 0.78 | 94 | SO4 |
| 3 | 532 | 0.72 | 0.81 | 52 | SO4 |
| 4 | 248 | 0.64 | 0.82 | 24 | empty |
| 5 | 93 | 0.50 | 0.82 | 16 | IPA |
Interfaces
5 interfaces between chains.
- B–D · 1474 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 1461 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 1078 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 233 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–D · 214 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 4HCC · The zinc ion bound 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 4HCC · PDBe 4HCC · UniProt P04995
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