MolNFT v1 · #159274 · protein
LTP2-CHSH2(DUF35) aldolase
6OK1 · Lipid-transfer protein: “LTP2-CHSH2(DUF35) aldolase”. X-ray diffraction, 3 ligands (NA, ZN, CL), 6 pockets (best druggability 0.76). MolNFT v1 #159274 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OK1
- Type
- protein
- Length
- 1,022 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipid-transfer protein; CHSH2(DUF35)
- UniProt
- D1AB74, D1AB77
- Ligands
- NA, ZN, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipid-transfer protein | protein | 382 | 38% helix, 19% strand | D1AB74 |
| B | CHSH2(DUF35) | protein | 131 | 8% helix, 41% strand | D1AB77 |
| C | Lipid-transfer protein | protein | 382 | 38% helix, 19% strand | D1AB74 |
| D | CHSH2(DUF35) | protein | 127 | 9% helix, 43% strand | D1AB77 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.76 | 0.78 | 137 | CL |
| 2 | 105 | 0.51 | 0.82 | 23 | empty |
| 3 | 125 | 0.50 | 0.80 | 29 | empty |
| 4 | 83 | 0.34 | 0.75 | 18 | empty |
| 5 | 60 | 0.31 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2120 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1597 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1562 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 495 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6OK1 · Ltp2-ChsH2(DUF35) aldolase · the same entry in another collection · chain D against D, TM-score 1.00
- D1AB77 · AlphaFold monomer V2.0 prediction for probable enoyl-CoA hydratase alpha subunit (D1AB77) · a predicted model of the same protein · chain D against A, TM-score 0.99
- D1AB74 · AlphaFold monomer V2.0 prediction for steroid side-chain-cleaving aldolase (D1AB74) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 D1AB74
- Every structure of UniProt D1AB77
- Elsewhere: RCSB PDB 6OK1 · PDBe 6OK1 · UniProt D1AB74 · UniProt D1AB77
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