MolNFT v1 · #107500 · protein
Neisseria meningitidis DAH7PS-phenylalanine regulated
4UC5 · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Neisseria meningitidis DAH7PS-phenylalanine regulated”. X-ray diffraction, 3 ligands (PHE, MN, SO4), 16 pockets (best druggability 0.72). MolNFT v1 #107500 on GenesisL1: 3D structure…
- PDB
- 4UC5
- Type
- protein
- Length
- 1,386 residues
- Chains
- 4
- 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
- Q9K169
- Ligands
- PHE, MN, SO4
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 346 | 39% helix, 18% strand | Q9K169 |
| C, D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 347 | 40% helix, 18% strand | Q9K169 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.72 | 0.84 | 72 | empty |
| 2 | 68 | 0.71 | 0.97 | 21 | empty |
| 3 | 274 | 0.71 | 0.85 | 55 | SO4 |
| 4 | 373 | 0.70 | 0.83 | 70 | SO4 |
| 5 | 65 | 0.70 | 0.96 | 20 | PHE |
Interfaces
6 interfaces between chains.
- A–B · 3468 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3435 Ų buried · 63 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UC5 · Neisseria Meningitidis DAH7PS-Phenylalanine regulated · 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 Q9K169
- Elsewhere: RCSB PDB 4UC5 · PDBe 4UC5 · UniProt Q9K169
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