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1.9 ångström crystal structure of the rat vap-a msp homology domain in complex with the rat ORP1 ffat motif
Analyse 1.9 ångström crystal structure of the rat vap-a msp homology domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z9O
- Type
- protein
- Length
- 768 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-associated membrane protein-associated protein a; Oxysterol binding protein
- UniProt
- Q8K4M9
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Vesicle-associated membrane protein-associated protein a | protein | 119 | 11% helix, 48% strand | — |
| G, H, I, J, K, L | Oxysterol binding protein | protein | 9 | 0% helix, 22% strand | Q8K4M9 |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.78 | 0.87 | 51 | empty |
| 2 | 439 | 0.77 | 0.86 | 54 | empty |
| 3 | 768 | 0.67 | 0.75 | 66 | empty |
| 4 | 521 | 0.65 | 0.77 | 55 | empty |
| 5 | 352 | 0.60 | 0.77 | 47 | empty |
Interfaces
21 interfaces between chains.
- E–K · 549 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 548 Ų buried · 7 hydrogen bonds · protein-protein
- C–I · 545 Ų buried · 7 hydrogen bonds · protein-protein
- F–L · 543 Ų buried · 7 hydrogen bonds · protein-protein
- D–J · 541 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1Z9O · 1.9 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain in Complex with the… · the same entry in another collection · chain K against K, 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 Q8K4M9
- Elsewhere: RCSB PDB 1Z9O · PDBe 1Z9O · UniProt Q8K4M9
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