Research workbench
Structure of the catspermasome
Analyse Structure of the catspermasome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EEB
- Type
- protein
- Length
- 6,003 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enhanced green fluorescent PROTEIN,CATION channel sperm- associated protein 1; Cation…
- UniProt
- Q91ZR5, A2ARP9, Q80W99, Q8BVN3, A2RTF1, C6KI89, E9Q9F6, P0DP43, Q3V161, A0A2R8VHF7, D3Z338, Q9DAM2, Q9CQP8
- Ligands
- 9Z9, NAG, BMA, NA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 14 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enhanced green fluorescent PROTEIN,CATION channel sperm- associated protein 1 | protein | 258 | 81% helix, 0% strand | Q91ZR5 |
| B | Cation channel sperm-associated protein 2 | protein | 281 | 77% helix, 0% strand | A2ARP9 |
| C | Cation channel sperm-associated protein 3 | protein | 278 | 83% helix, 0% strand | Q80W99 |
| D | Cation channel sperm-associated protein 4 | protein | 242 | 78% helix, 0% strand | Q8BVN3 |
| E | Cation channel sperm-associated protein subunit beta | protein | 1053 | 10% helix, 36% strand | A2RTF1 |
| F | Cation channel sperm-associated protein subunit gamma 2 | protein | 1042 | 15% helix, 36% strand | C6KI89 |
| G | Cation channel sperm-associated protein subunit delta | protein | 714 | 8% helix, 38% strand | E9Q9F6 |
| H | Cation channel sperm-associated protein subunit epsilon | protein | 916 | 12% helix, 37% strand | P0DP43 |
| L | Kazal-like domain-containing protein | protein | 597 | 66% helix, 4% strand | Q3V161 |
| J | Transmembrane protein 249 | protein | 161 | 33% helix, 17% strand | A0A2R8VHF7 |
| M | Transmembrane protein 262 | protein | 116 | 75% helix, 0% strand | D3Z338 |
| N | Unknown | protein | 28 | 64% helix, 0% strand | — |
| I | Ef-hand calcium-binding domain-containing protein 9 | protein | 174 | 60% helix, 5% strand | Q9DAM2 |
| K | Cation channel sperm-associated protein subunit zeta | protein | 143 | 76% helix, 0% strand | Q9CQP8 |
Ligands and binding sites
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · 3 copies · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 copies · chains E, F, G, H, L
- BMA · beta-D-mannopyranose · sugar · 21 copies · chains E, G, H
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
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 | 1097 | 0.88 | 0.89 | 108 | empty |
| 2 | 357 | 0.86 | 0.95 | 34 | NA |
| 3 | 559 | 0.85 | 0.90 | 72 | empty |
| 4 | 703 | 0.85 | 0.88 | 114 | empty |
| 5 | 686 | 0.84 | 0.88 | 89 | empty |
Interfaces
26 interfaces between chains.
- E–F · 3414 Ų buried · 31 hydrogen bonds · protein-protein
- F–H · 2083 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1999 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1846 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1828 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 25 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7EEB · Structure of the CatSpermasome · the same entry in another collection · chain G against G, 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 Q91ZR5
- Every structure of UniProt A2ARP9
- Every structure of UniProt Q80W99
- Every structure of UniProt Q8BVN3
- Every structure of UniProt A2RTF1
- Every structure of UniProt C6KI89
- Every structure of UniProt E9Q9F6
- Every structure of UniProt P0DP43
- Every structure of UniProt Q3V161
- Every structure of UniProt A0A2R8VHF7
- Every structure of UniProt D3Z338
- Every structure of UniProt Q9DAM2
- Every structure of UniProt Q9CQP8
- Elsewhere: RCSB PDB 7EEB · PDBe 7EEB · UniProt Q91ZR5 · UniProt A2ARP9 · UniProt Q80W99 · UniProt Q8BVN3 · UniProt A2RTF1 · UniProt C6KI89 · UniProt E9Q9F6 · UniProt P0DP43 · UniProt Q3V161 · UniProt A0A2R8VHF7 · UniProt D3Z338 · UniProt Q9DAM2 · UniProt Q9CQP8
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