MolNFT v1 · #82168 · protein
Rhodococcus jostii RHA1 dypb N246H variant in complex with heme
3VEF: “Rhodococcus jostii RHA1 dypb N246H variant in complex with heme”. X-ray diffraction, 2 ligands (HEM, CL), 14 pockets (best druggability 0.81). MolNFT v1 #82168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VEF
- Type
- protein
- Length
- 926 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dypb
- EC
- 1.11.1.-
- UniProt
- Q0SE24
- Ligands
- HEM, CL
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dypb (EC 1.11.1.-) | protein | 308 | 31% helix, 26% strand | Q0SE24 |
| B | Dypb (EC 1.11.1.-) | protein | 310 | 31% helix, 26% strand | Q0SE24 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.81 | 0.91 | 39 | HEM |
| 2 | 333 | 0.80 | 0.90 | 39 | HEM |
| 3 | 846 | 0.80 | 0.83 | 94 | HEM |
| 4 | 85 | 0.70 | 0.94 | 30 | empty |
| 5 | 329 | 0.61 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1240 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 815 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 387 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VEF · Rhodococcus jostii RHA1 DypB N246H variant in complex with heme · 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 Q0SE24
- Elsewhere: RCSB PDB 3VEF · PDBe 3VEF · UniProt Q0SE24
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