MolNFT v1 · #159616 · protein
Crystal structure of the disabled-2 (DAB2) dab homology domain in complex with peptide STA03
6OVF · Disabled homolog 2: “Crystal structure of the disabled-2 (DAB2) dab homology domain in complex with peptide STA03”. X-ray diffraction, 3 ligands (ACE, MG, NI), 1 pocket (best druggability 0.65). MolNFT v1 #159616 on GenesisL1: 3D…
- PDB
- 6OVF
- Type
- protein
- Length
- 331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disabled homolog 2; STA03
- UniProt
- P98082
- Ligands
- ACE, MG, NI
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Disabled homolog 2 | protein | 154 | 38% helix, 32% strand | P98082 |
| C | STA03 | protein | 11 | 0% helix, 18% strand | — |
| D | STA03 | protein | 12 | 0% helix, 17% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains D
- MG · Magnesium ion · metal · 3 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.65 | 0.75 | 54 | empty |
Interfaces
3 interfaces between chains.
- B–D · 863 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 803 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 288 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6OVF · Crystal Structure of the Disabled-2 (Dab2) Dab Homology Domain in Complex with Peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P98082 · AlphaFold monomer V2.0 prediction for disabled homolog 2 (P98082) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P98082
- Elsewhere: RCSB PDB 6OVF · PDBe 6OVF · UniProt P98082
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