Research workbench
Haddock model of GATA1NF:LMO2LIM2-LDB1LID with fog
Analyse Haddock model of GATA1NF:LMO2LIM2-LDB1LID with fog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2L6Z
- Type
- protein
- Length
- 171 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythroid transcription factor; Zinc finger protein ush; Lim domain only 2, linker, lim…
- UniProt
- P17679, Q9VPQ6, Q544Z2, P70662
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.38
Structure
solution nmr · 3 distinct chains · 11% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythroid transcription factor | protein | 39 | 13% helix, 5% strand | P17679 |
| B | Zinc finger protein ush | protein | 36 | 28% helix, 6% strand | Q9VPQ6 |
| C | Lim domain only 2, linker, lim domain-binding protein 1 | protein | 96 | 4% helix, 16% strand | Q544Z2, P70662 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.38 | 0.75 | 15 | empty |
| 2 | 73 | 0.31 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 520 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2L6Z · haddock model of GATA1NF:Lmo2LIM2-Ldb1LID with FOG · the same entry in another collection · chain A against A, TM-score 1.00
- P17679 · AlphaFold monomer V2.0 prediction for erythroid transcription factor (P17679) · a predicted model of the same protein · chain A against A, TM-score 0.58
- Q9VPQ6 · AlphaFold monomer V2.0 prediction for zinc finger protein ush (Q9VPQ6) · a predicted model of the same protein · chain B against A, TM-score 0.52
- P70662 · AlphaFold monomer V2.0 prediction for lim domain-binding protein 1 (P70662) · a predicted model of the same protein · chain C against A, TM-score 0.35
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 P17679
- Every structure of UniProt Q9VPQ6
- Every structure of UniProt Q544Z2
- Every structure of UniProt P70662
- Elsewhere: RCSB PDB 2L6Z · PDBe 2L6Z · UniProt P17679 · UniProt Q9VPQ6 · UniProt Q544Z2 · UniProt P70662
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