MolNFT v1 · #121146 · protein
Crystal structure of T5 D15 protein co-crystallized with metal ions
5HML · Exodeoxyribonuclease: “Crystal structure of T5 D15 protein co-crystallized with metal ions”. X-ray diffraction, 3 ligands (MG, CL, IOD), 4 pockets (best druggability 0.80). MolNFT v1 #121146 on GenesisL1: 3D structure, binding sites…
- PDB
- 5HML
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease
- EC
- 3.1.11.3
- UniProt
- P06229
- Ligands
- MG, CL, IOD
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exodeoxyribonuclease (EC 3.1.11.3) | protein | 271 | 63% helix, 10% strand | P06229 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B
- IOD · Iodide ion · ion · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.80 | 0.81 | 106 | CL, IOD |
| 2 | 322 | 0.60 | 0.78 | 34 | CL |
| 3 | 52 | 0.46 | 0.85 | 11 | CL |
| 4 | 88 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 978 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5HML · Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions · 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 P06229
- Elsewhere: RCSB PDB 5HML · PDBe 5HML · UniProt P06229
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