Research workbench
Structure of the biliverdin reductase RV2074 from mycobacterium tuberculosis in complex with F420
Analyse Structure of the biliverdin reductase RV2074 from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JAB
- Type
- protein
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biliverdin reductase RV2074
- UniProt
- P9WLL7
- Ligands
- 6J4, CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biliverdin reductase RV2074 | protein | 135 | 25% helix, 42% strand | P9WLL7 |
| B, C | Biliverdin reductase RV2074 | protein | 127 | 27% helix, 45% strand | P9WLL7 |
| D | Biliverdin reductase RV2074 | protein | 134 | 26% helix, 42% strand | P9WLL7 |
Ligands and binding sites
- 6J4 · Coenzyme F420-3 · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.72 | 0.75 | 85 | CL |
| 2 | 231 | 0.47 | 0.74 | 24 | CL |
| 3 | 104 | 0.43 | 0.78 | 14 | empty |
| 4 | 142 | 0.41 | 0.74 | 25 | 6J4, CL |
| 5 | 56 | 0.31 | 0.76 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 940 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 909 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 64 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JAB · Structure of the biliverdin reductase Rv2074 from Mycobacterium tuberculosis in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WLL7 · AlphaFold monomer V2.0 prediction for F420H(2)-dependent biliverdin reductase (P9WLL7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WLL7
- Elsewhere: RCSB PDB 5JAB · PDBe 5JAB · UniProt P9WLL7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.