Research workbench
Structure of the human endothelial nitric oxide synthase heme domain in complex with N-(1-(piperidin-4-YL)INDOLIN-5-YL)THIOPHENE-2- carboximidamide
Analyse Structure of the human endothelial nitric oxide synthase heme domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CIF
- Type
- protein
- Length
- 1,612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase, endothelial
- EC
- 1.14.13.39
- UniProt
- P29474
- Ligands
- HEM, H4B, F2J, GD, ZN, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 40% helix, 15% strand | P29474 |
| B | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 403 | 41% helix, 16% strand | P29474 |
| C | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 401 | 41% helix, 15% strand | P29474 |
| D | Nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 404 | 40% helix, 15% strand | P29474 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 4 copies · chains A, B, C, D
- F2J · N-[1-(piperidin-4-yl)-1H-indol-5-yl]thiophene-2-carboximidamide · ligand · 4 copies · chains A, B, C, D
- GD · Gadolinium atom · metal · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.85 | 0.86 | 84 | HEM, H4B, F2J, CL |
| 2 | 1071 | 0.85 | 0.86 | 92 | HEM, H4B, F2J, CL |
| 3 | 1039 | 0.85 | 0.86 | 93 | HEM, H4B, F2J, CL |
| 4 | 1103 | 0.85 | 0.85 | 92 | HEM, H4B, F2J, CL |
| 5 | 93 | 0.73 | 0.95 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2797 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2713 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 513 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 88 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6CIF · Structure of the human endothelial nitric oxide synthase heme domain in complex with… · 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 P29474
- Elsewhere: RCSB PDB 6CIF · PDBe 6CIF · UniProt P29474
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