MolNFT v1 · #121147 · protein
Crystal structure of T5 D15 protein co-crystallized with metal ions
5HMM · Exodeoxyribonuclease: “Crystal structure of T5 D15 protein co-crystallized with metal ions”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.82). MolNFT v1 #121147 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HMM
- Type
- protein
- Length
- 537 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
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease (EC 3.1.11.3) | protein | 266 | 59% helix, 11% strand | P06229 |
| B | Exodeoxyribonuclease (EC 3.1.11.3) | protein | 271 | 56% helix, 12% strand | P06229 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.82 | 0.84 | 111 | CL, MG |
| 2 | 283 | 0.59 | 0.78 | 29 | MG |
| 3 | 50 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5HMM · 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 5HMM · PDBe 5HMM · UniProt P06229
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.