MolNFT v1 · #154470 · protein
Crystal structure of human fer SH2 domain bound to a phosphopeptide (depyenvd)
6KC4 · Tyrosine-protein kinase fer: “Crystal structure of human fer SH2 domain bound to a phosphopeptide (depyenvd)”. X-ray diffraction, 7 pockets (best druggability 0.70). MolNFT v1 #154470 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KC4
- Type
- protein
- Length
- 641 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase fer; Phosphopeptide (edpyenvd)
- EC
- 2.7.10.2
- UniProt
- P16591
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G, K | Tyrosine-protein kinase fer (EC 2.7.10.2) | protein | 101 | 21% helix, 30% strand | P16591 |
| B, F, H, J, L | Phosphopeptide (edpyenvd) | protein | 6 | 0% helix, 0% strand | — |
| C, I | Tyrosine-protein kinase fer (EC 2.7.10.2) | protein | 100 | 21% helix, 30% strand | P16591 |
| D | Phosphopeptide (edpyenvd) | protein | 7 | 0% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.70 | 0.80 | 60 | empty |
| 2 | 844 | 0.70 | 0.76 | 87 | empty |
| 3 | 417 | 0.69 | 0.81 | 50 | empty |
| 4 | 98 | 0.44 | 0.79 | 23 | empty |
| 5 | 61 | 0.42 | 0.81 | 16 | empty |
Interfaces
20 interfaces between chains.
- C–D · 537 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 512 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 480 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 477 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 458 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 6KC4 · Crystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD) · the same entry in another collection · chain L against L, 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 P16591
- Elsewhere: RCSB PDB 6KC4 · PDBe 6KC4 · UniProt P16591
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