Research workbench
Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif
Analyse Crystal structure of the C-terminal calponin homology domain of alpha parvin in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VZD
- Type
- protein
- Length
- 279 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-parvin; Paxillin
- UniProt
- Q9NVD7, P49023
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-parvin | protein | 127 | 65% helix, 1% strand | Q9NVD7 |
| B | Alpha-parvin | protein | 126 | 64% helix, 1% strand | Q9NVD7 |
| C | Paxillin | protein | 12 | 75% helix, 0% strand | P49023 |
| D | Paxillin | protein | 14 | 71% helix, 0% strand | P49023 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.64 | 0.81 | 27 | EDO, GOL |
| 2 | 63 | 0.32 | 0.76 | 13 | empty |
| 3 | 56 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–D · 594 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 532 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2VZD · Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NVD7 · AlphaFold monomer V2.0 prediction for alpha-parvin (Q9NVD7) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P49023 · AlphaFold monomer V2.0 prediction for paxillin (P49023) · a predicted model of the same protein · chain C against A, TM-score 0.66
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 Q9NVD7
- Every structure of UniProt P49023
- Elsewhere: RCSB PDB 2VZD · PDBe 2VZD · UniProt Q9NVD7 · UniProt P49023
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