MolNFT v1 · #134220 · protein
WDR5 in complex with mll win motif peptidomimetic
5SXM · Wd repeat-containing protein 5: “WDR5 in complex with mll win motif peptidomimetic”. X-ray diffraction, 2 ligands (ACE, NH2), 4 pockets (best druggability 0.74). MolNFT v1 #134220 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5SXM
- Type
- protein
- Length
- 619 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; ACE-ala-arg-thr-glu-val-tyr-NH2
- UniProt
- P61964
- Ligands
- ACE, NH2
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 51% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 51% strand | P61964 |
| D, C | ACE-ala-arg-thr-glu-val-tyr-NH2 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, D, A, C
- NH2 · Amino group · ion · 2 copies · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.74 | 0.82 | 45 | empty |
| 2 | 485 | 0.73 | 0.82 | 48 | empty |
| 3 | 291 | 0.56 | 0.77 | 37 | empty |
| 4 | 145 | 0.43 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 558 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 557 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5SXM · WDR5 in complex with MLL Win motif peptidomimetic · the same entry in another collection · chain A against A, TM-score 1.00
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 P61964
- Elsewhere: RCSB PDB 5SXM · PDBe 5SXM · UniProt P61964
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