Research workbench
Crystal structure of mn-protoporphyrinix-reconstituted P450BM3
Analyse Crystal structure of mn-protoporphyrinix-reconstituted P450BM3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZIS
- Type
- protein
- Length
- 1,804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional cytochrome P450/NADPH--P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- MNH
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 452 | 53% helix, 12% strand | P14779 |
| B | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 449 | 53% helix, 10% strand | P14779 |
| D | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 451 | 53% helix, 12% strand | P14779 |
Ligands and binding sites
- MNH · Manganese protoporphyrin IX · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.89 | 0.93 | 88 | MNH |
| 2 | 637 | 0.88 | 0.92 | 91 | MNH |
| 3 | 1145 | 0.87 | 0.88 | 135 | MNH |
| 4 | 637 | 0.87 | 0.92 | 89 | MNH |
| 5 | 470 | 0.76 | 0.85 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1071 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1036 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 967 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 187 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZIS · Crystal structure of Mn-ProtoporphyrinIX-reconstituted P450BM3 · the same entry in another collection · chain D against D, TM-score 1.00
- P14779 · AlphaFold monomer V2.0 prediction for bifunctional cytochrome P450/NADPH--P450 reductase… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P14779
- Elsewhere: RCSB PDB 5ZIS · PDBe 5ZIS · UniProt P14779
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