MolNFT v1 · #157259 · protein
Synaptotagmin-1 C2A, C2B domains and snare-pin proteins (5CCI) individually docked into cryo-EM MAP of C2AB-snare complexes helically organized on lipid nanotube surface in presence of MG2+
6MTI: “Synaptotagmin-1 C2A, C2B domains and snare-pin proteins (5CCI) individually docked into cryo-EM MAP of…”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.72). MolNFT v1 #157259 on GenesisL1: 3D structure, binding…
- PDB
- 6MTI
- Type
- protein
- Length
- 2,966 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptotagmin-1; Vesicle-associated membrane protein 2; Syntaxin-1A…
- UniProt
- P21707, P63045, P32851, P60881
- Ligands
- MG
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 6 distinct chains · 43% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 6 | Synaptotagmin-1 | protein | 127 | 3% helix, 46% strand | P21707 |
| 2, 3, 4, 5 | Synaptotagmin-1 | protein | 279 | 9% helix, 46% strand | P21707 |
| A, E, I, M, Q, U | Vesicle-associated membrane protein 2 | protein | 62 | 97% helix, 0% strand | P63045 |
| B, F, J, N, R, V | Syntaxin-1A | protein | 67 | 96% helix, 0% strand | P32851 |
| C, G, K, O, S, W | Synaptosomal-associated protein 25 | protein | 73 | 97% helix, 0% strand | P60881 |
| D, H, L, P, T, X | Synaptosomal-associated protein 25 | protein | 64 | 95% helix, 0% strand | P60881 |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains 1, 2, 3, 4, 5, 6
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.72 | 0.76 | 90 | empty |
| 2 | 882 | 0.72 | 0.77 | 75 | empty |
| 3 | 624 | 0.65 | 0.76 | 54 | empty |
| 4 | 587 | 0.65 | 0.76 | 61 | empty |
| 5 | 210 | 0.65 | 0.84 | 30 | empty |
Interfaces
91 interfaces between chains.
- I–J · 1633 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1631 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 1630 Ų buried · 12 hydrogen bonds · protein-protein
- U–V · 1628 Ų buried · 12 hydrogen bonds · protein-protein
- Q–R · 1628 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6MTI · Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into… · the same entry in another collection · chain E against E, 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 P21707
- Every structure of UniProt P63045
- Every structure of UniProt P32851
- Every structure of UniProt P60881
- Elsewhere: RCSB PDB 6MTI · PDBe 6MTI · UniProt P21707 · UniProt P63045 · UniProt P32851 · UniProt P60881
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