MolNFT v1 · #126853 · protein
Designed armadillo repeat protein YIIIM''6AII in complex with PD_(KR)5
5MFD: “Designed armadillo repeat protein YIIIM''6AII in complex with PD_(KR)5”. X-ray diffraction, 1 ligand (CA), 19 pockets (best druggability 0.87). MolNFT v1 #126853 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MFD
- Type
- protein
- Length
- 3,005 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YIIIM''6AII; Capsid decoration PROTEIN,PD_(KR)5
- UniProt
- P03712
- Ligands
- CA
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, I, K, L | YIIIM''6AII | protein | 323 | 77% helix, 0% strand | — |
| B, F | Capsid decoration PROTEIN,PD_(KR)5 | protein | 105 | 8% helix, 31% strand | P03712 |
| D | Capsid decoration PROTEIN,PD_(KR)5 | protein | 107 | 7% helix, 35% strand | P03712 |
| G | YIIIM''6AII | protein | 322 | 79% helix, 0% strand | — |
| H | Capsid decoration PROTEIN,PD_(KR)5 | protein | 104 | 8% helix, 33% strand | P03712 |
| J | YIIIM''6AII | protein | 324 | 78% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 49 copies · chains A, C, B, E, I, F, G, J, H, K, D, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.87 | 0.88 | 95 | CA |
| 2 | 1178 | 0.86 | 0.87 | 100 | CA |
| 3 | 1196 | 0.76 | 0.78 | 102 | empty |
| 4 | 317 | 0.73 | 0.86 | 48 | CA |
| 5 | 197 | 0.66 | 0.85 | 32 | CA |
Interfaces
24 interfaces between chains.
- A–C · 1816 Ų buried · 53 hydrogen bonds · protein-protein
- K–L · 1800 Ų buried · 50 hydrogen bonds · protein-protein
- E–I · 1798 Ų buried · 53 hydrogen bonds · protein-protein
- G–J · 1736 Ų buried · 49 hydrogen bonds · protein-protein
- G–H · 1256 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5MFD · Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 · 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 P03712
- Elsewhere: RCSB PDB 5MFD · PDBe 5MFD · UniProt P03712
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