MolNFT v1 · #165527 · protein
Structure of human LDB1 in complex with SSBP2
6TYD · Lim domain-binding protein 1: “Structure of human LDB1 in complex with SSBP2”. X-ray diffraction, 4 pockets (best druggability 0.60). MolNFT v1 #165527 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TYD
- Type
- protein
- Length
- 371 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lim domain-binding protein 1; Single-stranded DNA-binding protein 2
- UniProt
- Q86U70, P81877
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | Lim domain-binding protein 1 | protein | 219 | 41% helix, 32% strand | Q86U70 |
| A | Single-stranded DNA-binding protein 2 | protein | 85 | 58% helix, 0% strand | P81877 |
| B | Single-stranded DNA-binding protein 2 | protein | 67 | 67% helix, 0% strand | P81877 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.60 | 0.78 | 44 | empty |
| 2 | 54 | 0.47 | 0.85 | 15 | empty |
| 3 | 59 | 0.43 | 0.82 | 18 | empty |
| 4 | 68 | 0.32 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1593 Ų buried · 14 hydrogen bonds · protein-protein
- V–A · 1061 Ų buried · 10 hydrogen bonds · protein-protein
- V–B · 773 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 6TYD · Structure of human LDB1 in complex with SSBP2 · the same entry in another collection · chain V against V, TM-score 1.00
- Q86U70 · AlphaFold monomer V2.0 prediction for lim domain-binding protein 1 (Q86U70) · a predicted model of the same protein · chain V against A, TM-score 0.97
- P81877 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein 2 (P81877) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q86U70
- Every structure of UniProt P81877
- Elsewhere: RCSB PDB 6TYD · PDBe 6TYD · UniProt Q86U70 · UniProt P81877
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