MolNFT v1 · #65192 · protein
Crystal structure of rhodocetin
3GPR · Rhodocetin subunit alpha: “Crystal structure of rhodocetin”. X-ray diffraction, 8 pockets (best druggability 0.53). MolNFT v1 #65192 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GPR
- Type
- protein
- Length
- 517 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodocetin subunit alpha; Rhodocetin subunit beta; Rhodocetin subunit gamma; Rhodocetin…
- UniProt
- P81397, P81398
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodocetin subunit alpha | protein | 132 | 16% helix, 29% strand | P81397 |
| B | Rhodocetin subunit beta | protein | 127 | 17% helix, 30% strand | P81398 |
| C | Rhodocetin subunit gamma | protein | 134 | 16% helix, 22% strand | — |
| D | Rhodocetin subunit delta | protein | 124 | 19% helix, 26% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.53 | 0.80 | 36 | empty |
| 2 | 115 | 0.53 | 0.83 | 22 | empty |
| 3 | 152 | 0.52 | 0.79 | 25 | empty |
| 4 | 177 | 0.47 | 0.76 | 24 | empty |
| 5 | 117 | 0.45 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1874 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1719 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 876 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 220 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 99 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3GPR · Crystal structure of rhodocetin · the same entry in another collection · chain A against A, TM-score 1.00
- P81398 · AlphaFold monomer V2.0 prediction for snaclec rhodocetin subunit beta (P81398) · a predicted model of the same protein · chain B against A, TM-score 0.91
- P81397 · AlphaFold monomer V2.0 prediction for snaclec rhodocetin subunit alpha (P81397) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 P81397
- Every structure of UniProt P81398
- Elsewhere: RCSB PDB 3GPR · PDBe 3GPR · UniProt P81397 · UniProt P81398
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