MolNFT v1 · #32459 · protein
Cmci-D160 mg-SAM
2BR4 · Cephalosporin hydroxylase cmci: “Cmci-D160 mg-SAM”. X-ray diffraction, 2 ligands (SAM, MG), 17 pockets (best druggability 0.75). MolNFT v1 #32459 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BR4
- Type
- protein
- Length
- 1,389 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cephalosporin hydroxylase cmci
- UniProt
- O85726
- Ligands
- SAM, MG
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cephalosporin hydroxylase cmci | protein | 231 | 32% helix, 19% strand | O85726 |
| B | Cephalosporin hydroxylase cmci | protein | 232 | 30% helix, 18% strand | O85726 |
| C | Cephalosporin hydroxylase cmci | protein | 232 | 32% helix, 18% strand | O85726 |
| D | Cephalosporin hydroxylase cmci | protein | 230 | 34% helix, 17% strand | O85726 |
| E | Cephalosporin hydroxylase cmci | protein | 233 | 30% helix, 17% strand | O85726 |
| F | Cephalosporin hydroxylase cmci | protein | 231 | 32% helix, 18% strand | O85726 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, E, B, C, D, F
- P4C · O-acetaldehydyl-hexaethylene glycol · additive · 3 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.75 | 0.78 | 86 | MG, SAM, PEG, P4C |
| 2 | 81 | 0.75 | 0.97 | 21 | empty |
| 3 | 1034 | 0.75 | 0.78 | 88 | MG, SAM, PEG, P4C |
| 4 | 68 | 0.74 | 0.98 | 21 | empty |
| 5 | 1140 | 0.74 | 0.77 | 89 | MG, SAM, PEG, P4C |
Interfaces
6 interfaces between chains.
- D–E · 2678 Ų buried · 44 hydrogen bonds · protein-protein
- C–F · 2660 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2622 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 2195 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 2162 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2BR4 · cmcI-D160 Mg-SAM · the same entry in another collection · chain B against B, 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 O85726
- Elsewhere: RCSB PDB 2BR4 · PDBe 2BR4 · UniProt O85726
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