MolNFT v1 · #159469 · protein
Crystal structure of CEP250 bound to FKBP12 in the presence of FK506- like novel natural product
6OQA · Peptidyl-prolyl cis-trans isomerase FKBP1A: “Crystal structure of CEP250 bound to FKBP12 in the presence of FK506- like novel natural product”. X-ray diffraction, 2 ligands (60Z, MG), 4 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 6OQA
- Type
- protein
- Length
- 767 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase FKBP1A; Centrosome-associated protein CEP250
- EC
- 5.2.1.8
- UniProt
- P62942, Q9BV73
- Ligands
- 60Z, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 108 | 9% helix, 40% strand | P62942 |
| B, E, F | Peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 107 | 10% helix, 40% strand | P62942 |
| C, D | Centrosome-associated protein CEP250 | protein | 83 | 96% helix, 0% strand | Q9BV73 |
| G | Centrosome-associated protein CEP250 | protein | 87 | 94% helix, 0% strand | Q9BV73 |
| H | Centrosome-associated protein CEP250 | protein | 85 | 98% helix, 0% strand | Q9BV73 |
Ligands and binding sites
- 60Z · (3r,4e,7e,10r,11s,12r,13s,16r,17r,24as)-11,17-dihydroxy-10,12,16-trimethyl-3-[(2R)-1-phenylbutan-2-yl]-6,9,10,11,12,13,14,15,16,17,22,23,24,24A-tetradecahydro-3H-13,17-epoxypyrido[2,1-C][1, 4]oxazacyclohenicosine-1,18,19(21H)-trione · ligand · 4 copies · chains A, C, D, B, E, G, H, F
- MG · Magnesium ion · metal · chains A, D
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, C, D, E, G, H
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, C, D, F, G, H
- PGE · Triethylene glycol · additive · 4 copies · chains B, A, C, D, E, G
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, C, B, D, G, H
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 2 copies · chains A, D, B
- MLA · Malonic acid · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.77 | 0.83 | 40 | 60Z, PG4 |
| 2 | 501 | 0.77 | 0.84 | 35 | 60Z, PGE |
| 3 | 562 | 0.76 | 0.82 | 42 | 60Z, PG4 |
| 4 | 544 | 0.76 | 0.83 | 37 | 60Z |
Interfaces
10 interfaces between chains.
- G–H · 2330 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2213 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 462 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 438 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 430 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6OQA · Crystal structure of CEP250 bound to FKBP12 in the presence of FK506-like novel natural… · the same entry in another collection · chain H against H, TM-score 1.00
- P62942 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1A (P62942) · a predicted model of the same protein · chain B 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 P62942
- Every structure of UniProt Q9BV73
- Elsewhere: RCSB PDB 6OQA · PDBe 6OQA · UniProt P62942 · UniProt Q9BV73
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