MolNFT v1 · #165856 · protein
Crystal structure of 3-deoxy-D-arabinoheptulosonate-7-phosphate SYNTHASE/PHOSPHO-2-dehydro-3-deoxyheptonate aldolase (ARO3) from candida auris
6U8J: “Crystal structure of 3-deoxy-D-arabinoheptulosonate-7-phosphate SYNTHASE/PHOSPHO-2-dehydro-3-deoxyheptonate…”. X-ray diffraction, 1 ligand (UNX), 20 pockets (best druggability 0.91). MolNFT v1 #165856 on GenesisL1: 3D structure…
- PDB
- 6U8J
- Type
- protein
- Length
- 2,957 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 2.5.1.54
- UniProt
- A0A2H0ZWN3
- Ligands
- UNX
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 372 | 39% helix, 18% strand | A0A2H0ZWN3 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 369 | 39% helix, 18% strand | A0A2H0ZWN3 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 374 | 39% helix, 17% strand | A0A2H0ZWN3 |
| F | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 371 | 38% helix, 18% strand | A0A2H0ZWN3 |
| G | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 369 | 38% helix, 18% strand | A0A2H0ZWN3 |
| H | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 358 | 37% helix, 18% strand | A0A2H0ZWN3 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.91 | 0.93 | 192 | empty |
| 2 | 772 | 0.90 | 0.94 | 118 | UNX |
| 3 | 794 | 0.90 | 0.93 | 122 | empty |
| 4 | 680 | 0.89 | 0.94 | 108 | empty |
| 5 | 417 | 0.84 | 0.91 | 76 | empty |
Interfaces
15 interfaces between chains.
- B–D · 3298 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 3286 Ų buried · 49 hydrogen bonds · protein-protein
- F–H · 3266 Ų buried · 46 hydrogen bonds · protein-protein
- E–G · 3082 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 519 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6U8J · Crystal structure of 3-deoxy-D-arabinoheptulosonate-7-phosphate… · the same entry in another collection · chain C against C, 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 A0A2H0ZWN3
- Elsewhere: RCSB PDB 6U8J · PDBe 6U8J · UniProt A0A2H0ZWN3
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