MolNFT v1 · #118742 · protein
Ligand binding domain 2 of penicillium marneffei MP1 protein complexed with multiple arachidonic acids
5FB7 · Envelope glycoprotein: “Ligand binding domain 2 of penicillium marneffei MP1 protein complexed with multiple arachidonic acids”. X-ray diffraction, 1 ligand (ACD), 11 pockets (best druggability 0.87). MolNFT v1 #118742 on GenesisL1…
- PDB
- 5FB7
- Type
- protein
- Length
- 612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein
- UniProt
- A0A093VKV7
- Ligands
- ACD
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Envelope glycoprotein | protein | 151 | 83% helix, 0% strand | A0A093VKV7 |
| C, D | Envelope glycoprotein | protein | 155 | 81% helix, 0% strand | A0A093VKV7 |
Ligands and binding sites
- ACD · Arachidonic acid · ligand · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.87 | 0.94 | 52 | ACD |
| 2 | 449 | 0.87 | 0.93 | 53 | ACD |
| 3 | 383 | 0.85 | 0.93 | 50 | ACD |
| 4 | 463 | 0.84 | 0.91 | 59 | ACD |
| 5 | 838 | 0.74 | 0.78 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–C · 737 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 712 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 431 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 393 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5FB7 · Ligand binding domain 2 of Penicillium marneffei MP1 protein complexed with multiple… · 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 A0A093VKV7
- Elsewhere: RCSB PDB 5FB7 · PDBe 5FB7 · UniProt A0A093VKV7
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