MolNFT v1 · #168555 · protein
Engineered carbene transferase rmanod Q52V, putative nitric oxide dioxygenase from rhodothermus marinus
6WK3: “Engineered carbene transferase rmanod Q52V, putative nitric oxide dioxygenase from rhodothermus marinus”. X-ray diffraction, 2 ligands (HEM, CU), 5 pockets (best druggability 0.87). MolNFT v1 #168555 on GenesisL1: 3D structure…
- PDB
- 6WK3
- Type
- protein
- Length
- 578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide dioxygenase
- EC
- 1.14.12.17
- UniProt
- D0MGT2
- Ligands
- HEM, CU
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitric oxide dioxygenase (EC 1.14.12.17) | protein | 145 | 84% helix, 0% strand | D0MGT2 |
| B | Nitric oxide dioxygenase (EC 1.14.12.17) | protein | 142 | 88% helix, 0% strand | D0MGT2 |
| D | Nitric oxide dioxygenase (EC 1.14.12.17) | protein | 146 | 82% helix, 0% strand | D0MGT2 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.87 | 0.88 | 83 | HEM, ACT |
| 2 | 453 | 0.79 | 0.87 | 38 | HEM, ACT |
| 3 | 471 | 0.78 | 0.85 | 42 | HEM, ACT |
| 4 | 685 | 0.72 | 0.78 | 57 | empty |
| 5 | 186 | 0.44 | 0.73 | 30 | CU |
Interfaces
4 interfaces between chains.
- A–B · 926 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 507 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WK3 · Engineered carbene transferase RmaNOD Q52V, putative nitric oxide dioxygenase from… · the same entry in another collection · chain B against B, 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 D0MGT2
- Elsewhere: RCSB PDB 6WK3 · PDBe 6WK3 · UniProt D0MGT2
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