MolNFT v1 · #35999 · protein
Crystal structure of the burkholderia glumae lipase-specific foldase in complex with its cognate lipase
2ES4: “Crystal structure of the burkholderia glumae lipase-specific foldase in complex with its cognate lipase”. X-ray diffraction, 2 ligands (CA, IOD), 12 pockets (best druggability 0.79). MolNFT v1 #35999 on GenesisL1: 3D structure…
- PDB
- 2ES4
- Type
- protein
- Length
- 1,178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase; Lipase chaperone
- EC
- 3.1.1.3
- UniProt
- Q05489, Q05490
- Ligands
- CA, IOD
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase (EC 3.1.1.3) | protein | 316 | 37% helix, 17% strand | Q05489 |
| D | Lipase chaperone | protein | 270 | 70% helix, 1% strand | Q05490 |
| B | Lipase (EC 3.1.1.3) | protein | 314 | 38% helix, 18% strand | Q05489 |
| E | Lipase chaperone | protein | 278 | 71% helix, 1% strand | Q05490 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.79 | 0.85 | 68 | IOD |
| 2 | 518 | 0.78 | 0.85 | 59 | empty |
| 3 | 227 | 0.76 | 0.90 | 44 | empty |
| 4 | 418 | 0.74 | 0.84 | 62 | empty |
| 5 | 228 | 0.65 | 0.83 | 46 | empty |
Interfaces
6 interfaces between chains.
- B–E · 2772 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2593 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 237 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 234 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 2ES4 · Crystal structure of the Burkholderia glumae lipase-specific foldase in complex with its… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05490 · AlphaFold monomer V2.0 prediction for lipase-specific foldase (Q05490) · a predicted model of the same protein · chain E 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 Q05489
- Every structure of UniProt Q05490
- Elsewhere: RCSB PDB 2ES4 · PDBe 2ES4 · UniProt Q05489 · UniProt Q05490
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