Research workbench
Rhodocetin in complex with the integrin ALPHA2-a domain with calcium
Analyse Rhodocetin in complex with the integrin ALPHA2-a domain with calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ND9
- 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
- CA, NA, SO4, CL, NH4
- Pockets
- 20 · best druggability 0.79
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, 33% 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 | 41% helix, 21% strand | P17301 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains C, F, I, L, O, R
- NA · Sodium ion · metal · 5 copies · chains C, F, I, L, O
- SO4 · Sulfate ion · ion · 16 copies · chains A, I, B, C, D, E, F, G, H, J, K, L, N, O, Q, R
- CL · Chloride ion · ion · 3 copies · chains E, F, H, I, J
- NH4 · Ammonium ion · ion · chains D
- GOL · Glycerol · additive · 2 copies · chains J, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.79 | 0.85 | 87 | SO4, CA, NA |
| 2 | 956 | 0.76 | 0.79 | 73 | empty |
| 3 | 417 | 0.74 | 0.84 | 48 | SO4 |
| 4 | 462 | 0.73 | 0.82 | 47 | CA, SO4, NA |
| 5 | 584 | 0.72 | 0.80 | 52 | CA, SO4, NA |
Interfaces
34 interfaces between chains.
- J–K · 2065 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2057 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2052 Ų buried · 38 hydrogen bonds · protein-protein
- P–Q · 2027 Ų buried · 37 hydrogen bonds · protein-protein
- M–N · 2025 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 6ND9 · Rhodocetin in complex with the integrin ALPHA2-a domain with calcium · 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 6ND9 · PDBe 6ND9 · UniProt D2YW39 · UniProt D2YW40 · UniProt P17301
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