MolNFT v1 · #127965 · protein
Enah EVH1 in complex with ac-wpppptedel-NH2
5NC7 · Protein enabled homolog: “Enah EVH1 in complex with ac-wpppptedel-NH2”. X-ray diffraction, 2 ligands (ACE, NH2), 6 pockets (best druggability 0.54). MolNFT v1 #127965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NC7
- Type
- protein
- Length
- 503 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein enabled homolog; Acta-derived 10-mer ac-fpppptedel-NH2 with acetylated (ac) and…
- UniProt
- Q8N8S7
- Ligands
- ACE, NH2
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein enabled homolog | protein | 109 | 16% helix, 49% strand | Q8N8S7 |
| B, C, D | Protein enabled homolog | protein | 110 | 18% helix, 48% strand | Q8N8S7 |
| K, I, J, L | Acta-derived 10-mer ac-fpppptedel-NH2 with acetylated (ac) and amidated (NH2) termini. phe is substitued by TRP to increase affinity for crystallization | protein | 10 | 0% helix, 0% strand | — |
| Z | Acta-derived 10-mer ac-fpppptedel-NH2 with acetylated (ac) and amidated (NH2) termini. phe is substitued by TRP to increase affinity for crystallization | protein | 6 | 0% helix, 0% strand | — |
| X, W | Acta-derived 10-mer ac-fpppptedel-NH2 with acetylated (ac) and amidated (NH2) termini. phe is substitued by TRP to increase affinity for crystallization | protein | 7 | 0% helix, 0% strand | — |
| Y | Acta-derived 10-mer ac-fpppptedel-NH2 with acetylated (ac) and amidated (NH2) termini. phe is substitued by TRP to increase affinity for crystallization | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 7 copies · chains C, K, A, B, I, J, D, L, Z, X, W
- NH2 · Amino group · ion · 4 copies · chains K, I, B, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.54 | 0.76 | 25 | empty |
| 2 | 256 | 0.54 | 0.76 | 22 | empty |
| 3 | 262 | 0.50 | 0.74 | 39 | ACE |
| 4 | 202 | 0.48 | 0.75 | 24 | ACE |
| 5 | 51 | 0.42 | 0.82 | 16 | ACE |
Interfaces
14 interfaces between chains.
- A–B · 568 Ų buried · 9 hydrogen bonds · protein-protein
- B–J · 561 Ų buried · 4 hydrogen bonds · protein-protein
- D–L · 537 Ų buried · 3 hydrogen bonds · protein-protein
- C–K · 536 Ų buried · 4 hydrogen bonds · protein-protein
- A–I · 523 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 5NC7 · ENAH EVH1 in complex with Ac-WPPPPTEDEL-NH2 · the same entry in another collection · chain W against W, 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 Q8N8S7
- Elsewhere: RCSB PDB 5NC7 · PDBe 5NC7 · UniProt Q8N8S7
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