MolNFT v1 · #137390 · protein
Crystal structure of ligy from sphingobium sp. strain syk-6
5VN5 · 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta…: “Crystal structure of ligy from sphingobium sp. strain syk-6”. X-ray diffraction, 2 ligands (ZN, CL), 11 pockets (best druggability 0.75). MolNFT v1 #137390 on GenesisL1: 3D…
- PDB
- 5VN5
- Type
- protein
- Length
- 998 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta- cleavage compound hydrolase
- UniProt
- G2IN02
- Ligands
- ZN, CL
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta- cleavage compound hydrolase | protein | 332 | 47% helix, 10% strand | G2IN02 |
| C | 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta- cleavage compound hydrolase | protein | 334 | 46% helix, 10% strand | G2IN02 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.75 | 0.80 | 73 | empty |
| 2 | 180 | 0.70 | 0.89 | 33 | empty |
| 3 | 375 | 0.70 | 0.82 | 29 | empty |
| 4 | 392 | 0.68 | 0.81 | 41 | CL |
| 5 | 146 | 0.55 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2266 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VN5 · Crystal structure of LigY from Sphingobium sp. strain SYK-6 · 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 G2IN02
- Elsewhere: RCSB PDB 5VN5 · PDBe 5VN5 · UniProt G2IN02
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