MolNFT v1 · #159708 · protein
Crystal structure of mray bound to carbacaprazamycin
6OYH · Mrayaa nanobody: “Crystal structure of mray bound to carbacaprazamycin”. X-ray diffraction, 1 ligand (NK4), 20 pockets (best druggability 0.83). MolNFT v1 #159708 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OYH
- Type
- protein
- Length
- 1,821 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mrayaa nanobody; Phospho-N-acetylmuramoyl-pentapeptide-transferase
- EC
- 2.7.8.13
- UniProt
- O66465
- Ligands
- NK4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Mrayaa nanobody | protein | 124 | 7% helix, 50% strand | — |
| A | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 326 | 73% helix, 2% strand | O66465 |
| G, F | Mrayaa nanobody | protein | 125 | 10% helix, 47% strand | — |
| C | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 328 | 72% helix, 2% strand | O66465 |
| B | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 330 | 72% helix, 2% strand | O66465 |
| H | Mrayaa nanobody | protein | 126 | 7% helix, 48% strand | — |
| D | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 337 | 72% helix, 1% strand | O66465 |
Ligands and binding sites
- NK4 · (5S)-5'-O-(5-amino-5-deoxy-beta-D-ribofuranosyl)-5'-C-[(2S,5S,6S)-5-carboxy-6-heptadecyl-1,4-dimethyl-3-oxo-1,4-diazepan-2-yl]uridine · ligand · 4 copies · chains A, C, B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.83 | 0.83 | 59 | empty |
| 2 | 954 | 0.83 | 0.83 | 63 | empty |
| 3 | 161 | 0.67 | 0.87 | 37 | empty |
| 4 | 56 | 0.67 | 0.95 | 21 | empty |
| 5 | 80 | 0.62 | 0.90 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1567 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1517 Ų buried · 14 hydrogen bonds · protein-protein
- F–B · 711 Ų buried · 11 hydrogen bonds · protein-protein
- E–A · 707 Ų buried · 11 hydrogen bonds · protein-protein
- G–C · 684 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6OYH · Crystal structure of MraY bound to carbacaprazamycin · the same entry in another collection · chain D against D, TM-score 1.00
- O66465 · AlphaFold monomer V2.0 prediction for phospho-N-acetylmuramoyl- pentapeptide-transferase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O66465
- Elsewhere: RCSB PDB 6OYH · PDBe 6OYH · UniProt O66465
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