Research workbench
Crystal structure of mray bound to capuramycin
Analyse Crystal structure of mray bound to capuramycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OYZ
- Type
- protein
- Length
- 1,749 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
- NKM
- 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, F | Mrayaa nanobody | protein | 124 | 5% helix, 48% strand | — |
| A | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 313 | 73% helix, 2% strand | O66465 |
| G | Mrayaa nanobody | protein | 125 | 7% helix, 47% strand | — |
| C | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 306 | 75% 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 | 123 | 7% helix, 49% strand | — |
| D | Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) | protein | 304 | 75% helix, 2% strand | O66465 |
Ligands and binding sites
- NKM · (2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S}, 3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.83 | 0.83 | 65 | empty |
| 2 | 1073 | 0.83 | 0.83 | 72 | empty |
| 3 | 54 | 0.71 | 0.98 | 20 | empty |
| 4 | 144 | 0.69 | 0.89 | 32 | empty |
| 5 | 52 | 0.68 | 0.97 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1460 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1400 Ų buried · 18 hydrogen bonds · protein-protein
- E–A · 718 Ų buried · 8 hydrogen bonds · protein-protein
- G–C · 698 Ų buried · 9 hydrogen bonds · protein-protein
- H–D · 667 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6OYZ · Crystal structure of MraY bound to capuramycin · 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 D 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 O66465
- Elsewhere: RCSB PDB 6OYZ · PDBe 6OYZ · UniProt O66465
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