MolNFT v1 · #25027 · protein
Structure-based functional identification of a novel heme- binding protein from thermus thermophilus HB8
1VDH · Muconolactone isomerase-like protein: “Structure-based functional identification of a novel heme- binding protein from thermus thermophilus HB8”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #25027 on GenesisL1…
- PDB
- 1VDH
- Type
- protein
- Length
- 1,235 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Muconolactone isomerase-like protein
- UniProt
- Q5SHL6
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Muconolactone isomerase-like protein | protein | 247 | 38% helix, 32% strand | Q5SHL6 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.72 | 0.81 | 48 | empty |
| 2 | 471 | 0.72 | 0.81 | 47 | empty |
| 3 | 499 | 0.71 | 0.80 | 43 | empty |
| 4 | 439 | 0.70 | 0.81 | 42 | empty |
| 5 | 442 | 0.70 | 0.80 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1865 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1841 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1772 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1772 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1754 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1VDH · Structure-based functional identification of a novel heme-binding protein from thermus… · the same entry in another collection · chain E against E, TM-score 1.00
- Q5SHL6 · AlphaFold monomer V2.0 prediction for coproheme decarboxylase (Q5SHL6) · a predicted model of the same protein · chain E 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 Q5SHL6
- Elsewhere: RCSB PDB 1VDH · PDBe 1VDH · UniProt Q5SHL6
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