MolNFT v1 · #123121 · protein
Structure of the biliverdin reductase RV2074 from mycobacterium tuberculosis in complex with F420
5JAB: “Structure of the biliverdin reductase RV2074 from mycobacterium tuberculosis in complex with F420”. X-ray diffraction, 2 ligands (6J4, CL), 6 pockets (best druggability 0.72). MolNFT v1 #123121 on GenesisL1: 3D structure, binding…
- 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
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