Research workbench
Rhodocetin in complex with the integrin ALPHA2-a domain with yttrium bound
Analyse Rhodocetin in complex with the integrin ALPHA2-a domain with yttrium bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NDG
- 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
- Y1, NA, SO4, CL, NH4
- Pockets
- 20 · best druggability 0.77
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 | 17% helix, 37% strand | D2YW40 |
| C, F, I, L, O, R | Integrin alpha-2 | protein | 191 | 43% helix, 22% strand | P17301 |
Ligands and binding sites
- Y1 · Yttrium 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, G, O, E, F, 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
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.77 | 0.81 | 74 | CL, SO4, Y1, NA |
| 2 | 703 | 0.76 | 0.81 | 90 | empty |
| 3 | 856 | 0.75 | 0.79 | 59 | empty |
| 4 | 767 | 0.73 | 0.79 | 70 | SO4, NA |
| 5 | 615 | 0.73 | 0.80 | 66 | SO4, Y1, NA |
Interfaces
34 interfaces between chains.
- A–B · 2071 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2058 Ų buried · 36 hydrogen bonds · protein-protein
- J–K · 2054 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 2018 Ų buried · 36 hydrogen bonds · protein-protein
- M–N · 2017 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 6NDG · Rhodocetin in complex with the integrin ALPHA2-a domain with yttrium bound · 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 6NDG · PDBe 6NDG · UniProt D2YW39 · UniProt D2YW40 · UniProt P17301
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