MolNFT v1 · #53318 · protein
Dodecahedral assembly of mhpd
2WQT · 2-keto-4-pentenoate hydratase: “Dodecahedral assembly of mhpd”. X-ray diffraction, 3 ligands (NA, K, PO4), 20 pockets (best druggability 0.88). MolNFT v1 #53318 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WQT
- Type
- protein
- Length
- 5,240 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-4-pentenoate hydratase
- EC
- 4.2.1.80
- UniProt
- P77608
- Ligands
- NA, K, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | 2-keto-4-pentenoate hydratase (EC 4.2.1.80) | protein | 262 | 32% helix, 32% strand | P77608 |
Ligands and binding sites
- NA · Sodium ion · metal · 20 copies · chains A, C, M, D, E, F, N, B, G, I, R, K, L, T, O, P, Q, H, S
- K · Potassium ion · metal · 20 copies · chains A, B, C, M, D, E, F, N, G, I, R, K, L, T, P, Q, S
- PO4 · Phosphate ion · ion · 38 copies · chains A, B, G, C, D, E, F, N, H, S, I, J, K, R, L, T, M, O, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.88 | 0.89 | 140 | K, NA, PO4 |
| 2 | 1199 | 0.88 | 0.89 | 148 | K, NA, PO4 |
| 3 | 650 | 0.80 | 0.84 | 74 | NA |
| 4 | 656 | 0.80 | 0.84 | 78 | K, NA |
| 5 | 655 | 0.79 | 0.84 | 80 | K, NA |
Interfaces
35 interfaces between chains.
- K–L · 848 Ų buried · 17 hydrogen bonds · protein-protein
- M–O · 845 Ų buried · 14 hydrogen bonds · protein-protein
- H–J · 843 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 838 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 837 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2WQT · Dodecahedral assembly of MhpD · the same entry in another collection · chain T against T, 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 P77608
- Elsewhere: RCSB PDB 2WQT · PDBe 2WQT · UniProt P77608
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