MolNFT v1 · #108270 · protein
Heterocyclase in complex with substrate and cofactor
4V1V · Lynd: “Heterocyclase in complex with substrate and cofactor”. X-ray diffraction, 3 ligands (ANP, MG, ZN), 19 pockets (best druggability 0.84). MolNFT v1 #108270 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4V1V
- Type
- protein
- Length
- 1,521 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lynd
- UniProt
- A0YXD2
- Ligands
- ANP, MG, ZN
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lynd | protein | 747 | 38% helix, 18% strand | A0YXD2 |
| B | Lynd | protein | 747 | 38% helix, 18% strand | A0YXD2 |
| C | Lynd | protein | 14 | 29% helix, 29% strand | — |
| D | Lynd | protein | 13 | 0% helix, 31% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.84 | 0.87 | 89 | ANP, MG |
| 2 | 916 | 0.84 | 0.86 | 95 | ANP, MG |
| 3 | 83 | 0.75 | 0.97 | 20 | empty |
| 4 | 72 | 0.74 | 0.98 | 18 | empty |
| 5 | 563 | 0.71 | 0.80 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3529 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 719 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 676 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 161 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 160 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4V1V · Heterocyclase in complex with substrate and Cofactor · 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 A0YXD2
- Elsewhere: RCSB PDB 4V1V · PDBe 4V1V · UniProt A0YXD2
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