MolNFT v1 · #115730 · protein
Ligand binding domain 2 of penicillium marneffei MP1 protein in complex with arachidonic acids
5CSD · Envelope glycoprotein: “Ligand binding domain 2 of penicillium marneffei MP1 protein in complex with arachidonic acids”. X-ray diffraction, 1 ligand (ACD), 13 pockets (best druggability 0.86). MolNFT v1 #115730 on GenesisL1: 3D…
- PDB
- 5CSD
- Type
- protein
- Length
- 633 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein
- UniProt
- A0A093VKV7
- Ligands
- ACD
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein | protein | 158 | 79% helix, 0% strand | A0A093VKV7 |
| D | Envelope glycoprotein | protein | 159 | 79% helix, 0% strand | A0A093VKV7 |
Ligands and binding sites
- ACD · Arachidonic acid · ligand · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.86 | 0.94 | 47 | ACD |
| 2 | 409 | 0.86 | 0.93 | 48 | ACD |
| 3 | 255 | 0.83 | 0.94 | 33 | ACD |
| 4 | 375 | 0.80 | 0.89 | 52 | ACD |
| 5 | 1105 | 0.78 | 0.80 | 90 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 779 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 753 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 379 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 349 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5CSD · Ligand binding domain 2 of Penicillium marneffei MP1 protein in complex with arachidonic… · the same entry in another collection · chain C against C, 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 5CSD · PDBe 5CSD · UniProt A0A093VKV7
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