MolNFT v1 · #116965 · protein
Crystal structure of dendroaspis polylepis mambalgin-1 wild-type in P21 space group.
5DU1: “Crystal structure of dendroaspis polylepis mambalgin-1 wild-type in P21 space group.”. X-ray diffraction, 2 pockets (best druggability 0.79). MolNFT v1 #116965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DU1
- Type
- protein
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mambalgin-1
- UniProt
- P0DKR6
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mambalgin-1 | protein | 57 | 5% helix, 49% strand | P0DKR6 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.79 | 0.87 | 37 | empty |
| 2 | 483 | 0.73 | 0.82 | 48 | empty |
Interfaces
6 interfaces between chains.
- C–D · 606 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 584 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 451 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 376 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 357 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5DU1 · Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P21 space group. · the same entry in another collection · chain D against D, TM-score 1.00
- P0DKR6 · AlphaFold monomer V2.0 prediction for mambalgin-1 (P0DKR6) · a predicted model of the same protein · chain C against A, TM-score 0.78
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 P0DKR6
- Elsewhere: RCSB PDB 5DU1 · PDBe 5DU1 · UniProt P0DKR6
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