Research workbench
Human VPS33A in complex with a fragment of human VPS16
Analyse Human VPS33A in complex with a fragment of human VPS16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BX9
- Type
- protein
- Length
- 1,250 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 33A; Vacuolar protein sorting-associated…
- UniProt
- Q96AX1, Q9H269
- Ligands
- LMR
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 33A | protein | 574 | 50% helix, 15% strand | Q96AX1 |
| B | Vacuolar protein sorting-associated protein 33A | protein | 581 | 50% helix, 15% strand | Q96AX1 |
| C | Vacuolar protein sorting-associated protein 16 homolog | protein | 95 | 76% helix, 0% strand | Q9H269 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, B
- MLA · Malonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.82 | 0.83 | 90 | empty |
| 2 | 437 | 0.72 | 0.82 | 38 | empty |
| 3 | 197 | 0.60 | 0.81 | 28 | empty |
| 4 | 77 | 0.60 | 0.89 | 17 | empty |
| 5 | 164 | 0.59 | 0.82 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1230 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 928 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4BX9 · Human Vps33A in complex with a fragment of human Vps16 · the same entry in another collection · chain A against A, TM-score 1.00
- Q96AX1 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 33A… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9H269 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 16… · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q96AX1
- Every structure of UniProt Q9H269
- Elsewhere: RCSB PDB 4BX9 · PDBe 4BX9 · UniProt Q96AX1 · UniProt Q9H269
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