MolNFT v1 · #141935 · protein
Structure of MDR3 dd with mbp tag mutant-I387V
5ZNZ · Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor…: “Structure of MDR3 dd with mbp tag mutant-I387V”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.80). MolNFT v1 #141935 on GenesisL1: 3D structure…
- PDB
- 5ZNZ
- Type
- protein
- Length
- 1,803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25
- UniProt
- P0AEX9, B1AWN9
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25 | protein | 449 | 51% helix, 17% strand | P0AEX9, B1AWN9 |
| B | Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25 | protein | 451 | 50% helix, 17% strand | P0AEX9, B1AWN9 |
| C | Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25 | protein | 450 | 50% helix, 17% strand | P0AEX9, B1AWN9 |
| D | Maltose-binding periplasmic PROTEIN,TUMOR necrosis factor receptor superfamily, member 25 | protein | 453 | 49% helix, 17% strand | P0AEX9, B1AWN9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 26 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.80 | 0.82 | 85 | SO4 |
| 2 | 1126 | 0.77 | 0.79 | 98 | SO4 |
| 3 | 1197 | 0.76 | 0.78 | 84 | SO4 |
| 4 | 1041 | 0.75 | 0.78 | 87 | SO4 |
| 5 | 596 | 0.70 | 0.78 | 73 | SO4 |
Interfaces
6 interfaces between chains.
- A–D · 1334 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1329 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 628 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 583 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 196 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZNZ · Structure of mDR3 DD with MBP tag mutant-I387V · 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 P0AEX9
- Every structure of UniProt B1AWN9
- Elsewhere: RCSB PDB 5ZNZ · PDBe 5ZNZ · UniProt P0AEX9 · UniProt B1AWN9
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