Research workbench
Rhodococcus jostii RHA1 dypb D153H variant in complex with heme
Analyse Rhodococcus jostii RHA1 dypb D153H variant in complex with heme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VED
- 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
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dypb (EC 1.11.1.-) | protein | 308 | 31% helix, 26% strand | Q0SE24 |
| B, C | Dypb (EC 1.11.1.-) | protein | 309 | 32% helix, 25% strand | Q0SE24 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.81 | 0.91 | 39 | HEM, CL |
| 2 | 318 | 0.80 | 0.91 | 40 | HEM, CL |
| 3 | 931 | 0.80 | 0.82 | 113 | HEM, CL |
| 4 | 147 | 0.74 | 0.92 | 33 | empty |
| 5 | 471 | 0.71 | 0.81 | 51 | CL, GOL |
Interfaces
3 interfaces between chains.
- A–B · 1237 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 805 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VED · Rhodococcus jostii RHA1 DypB D153H 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 3VED · PDBe 3VED · UniProt Q0SE24
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