MolNFT v1 · #157872 · protein
Rhodocetin in complex with the integrin ALPHA2-a domain and cobalt
6NDB · Snaclec rhodocetin subunit gamma: “Rhodocetin in complex with the integrin ALPHA2-a domain and cobalt”. X-ray diffraction, 5 ligands (CO, NA, SO4), 19 pockets (best druggability 0.83). MolNFT v1 #157872 on GenesisL1: 3D structure…
- PDB
- 6NDB
- Type
- protein
- Length
- 2,664 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snaclec rhodocetin subunit gamma; Snaclec rhodocetin subunit delta; Integrin alpha-2
- UniProt
- D2YW39, D2YW40, P17301
- Ligands
- CO, NA, SO4, CL, NH4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P | Snaclec rhodocetin subunit gamma | protein | 131 | 21% helix, 31% strand | D2YW39 |
| B, E, H, K, N, Q | Snaclec rhodocetin subunit delta | protein | 122 | 19% helix, 38% strand | D2YW40 |
| C, F, I, L, O, R | Integrin alpha-2 | protein | 191 | 42% helix, 21% strand | P17301 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 6 copies · chains C, F, I, L, O, R
- NA · Sodium ion · metal · 6 copies · chains C, F, I, L, O, R
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, N, O, Q, R
- CL · Chloride ion · ion · 9 copies · chains C, O, E, F, G, H, I, J, K, L, M, N, R
- NH4 · Ammonium ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.83 | 0.84 | 136 | CL, SO4, CO, NA |
| 2 | 876 | 0.75 | 0.79 | 58 | empty |
| 3 | 582 | 0.72 | 0.80 | 56 | SO4, CO, NA |
| 4 | 654 | 0.72 | 0.79 | 63 | SO4, NA |
| 5 | 576 | 0.71 | 0.80 | 50 | SO4, NA |
Interfaces
34 interfaces between chains.
- A–B · 2059 Ų buried · 38 hydrogen bonds · protein-protein
- J–K · 2058 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2044 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2018 Ų buried · 35 hydrogen bonds · protein-protein
- P–Q · 2017 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 6NDB · Rhodocetin in complex with the integrin ALPHA2-a domain and cobalt · the same entry in another collection · chain R against R, 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 D2YW39
- Every structure of UniProt D2YW40
- Every structure of UniProt P17301
- Elsewhere: RCSB PDB 6NDB · PDBe 6NDB · UniProt D2YW39 · UniProt D2YW40 · UniProt P17301
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