Research workbench
Rhodococcus jostii RHA1 dypb R244L variant in complex with heme
Analyse Rhodococcus jostii RHA1 dypb R244L 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
- 3VEG
- Type
- protein
- Length
- 927 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
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 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 | Dypb (EC 1.11.1.-) | protein | 310 | 32% helix, 26% strand | Q0SE24 |
| C | Dypb (EC 1.11.1.-) | protein | 309 | 30% helix, 25% 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
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.83 | 0.91 | 37 | HEM |
| 2 | 360 | 0.82 | 0.91 | 38 | HEM |
| 3 | 1023 | 0.81 | 0.82 | 112 | HEM |
| 4 | 141 | 0.73 | 0.92 | 34 | empty |
| 5 | 475 | 0.71 | 0.81 | 51 | CL |
Interfaces
3 interfaces between chains.
- A–B · 1235 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 812 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VEG · Rhodococcus jostii RHA1 DypB R244L 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 3VEG · PDBe 3VEG · UniProt Q0SE24
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