MolNFT v1 · #134365 · protein
Crystal structure of native tarin lectin
5T1X: “Crystal structure of native tarin lectin”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1 #134365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5T1X
- Type
- protein
- Length
- 869 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- A5HMM7
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Lectin | protein | 109 | 0% helix, 44% strand | A5HMM7 |
| B, F | Lectin | protein | 110 | 0% helix, 43% strand | — |
| C | Lectin | protein | 107 | 0% helix, 44% strand | A5HMM7 |
| D, H | Lectin | protein | 108 | 0% helix, 44% strand | — |
| G | Lectin | protein | 108 | 0% helix, 44% strand | A5HMM7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains B, F, D, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains E, F
- PGE · Triethylene glycol · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.71 | 0.81 | 61 | empty |
| 2 | 473 | 0.70 | 0.81 | 61 | empty |
| 3 | 150 | 0.50 | 0.78 | 22 | EDO |
| 4 | 158 | 0.49 | 0.77 | 23 | EDO |
| 5 | 131 | 0.47 | 0.78 | 28 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1831 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1778 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1753 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1721 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 1079 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 A5HMM7
- Elsewhere: RCSB PDB 5T1X · PDBe 5T1X · UniProt A5HMM7
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