MolNFT v1 · #55333 · protein
Pyrobaculum calidifontis esterase monoclinic form
2YH2: “Pyrobaculum calidifontis esterase monoclinic form”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.86). MolNFT v1 #55333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YH2
- Type
- protein
- Length
- 1,227 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- EC
- 3.1.1.1
- UniProt
- Q8NKS0
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Esterase (EC 3.1.1.1) | protein | 308 | 43% helix, 20% strand | Q8NKS0 |
| B | Esterase (EC 3.1.1.1) | protein | 307 | 43% helix, 21% strand | Q8NKS0 |
| C | Esterase (EC 3.1.1.1) | protein | 305 | 45% helix, 22% strand | Q8NKS0 |
| D | Esterase (EC 3.1.1.1) | protein | 307 | 44% helix, 21% strand | Q8NKS0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.86 | 0.88 | 107 | empty |
| 2 | 747 | 0.78 | 0.82 | 74 | empty |
| 3 | 407 | 0.77 | 0.86 | 54 | empty |
| 4 | 502 | 0.77 | 0.84 | 55 | empty |
| 5 | 659 | 0.76 | 0.81 | 68 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1356 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1309 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 567 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 561 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 319 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2YH2 · Pyrobaculum calidifontis esterase monoclinic form · the same entry in another collection · chain A against A, 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 Q8NKS0
- Elsewhere: RCSB PDB 2YH2 · PDBe 2YH2 · UniProt Q8NKS0
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