MolNFT v1 · #122341 · protein
Crystal structure of designed two-component self-assembling icosahedral cage I53-40
5IM5 · Designed riboflavin synthase: “Crystal structure of designed two-component self-assembling icosahedral cage I53-40”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #122341 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IM5
- Type
- protein
- Length
- 5,245 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed riboflavin synthase; Designed keto-hydroxyglutarate-ALDOLASE/KETO-deoxy…
- EC
- 2.5.1.9, 4.1.3.16
- UniProt
- Q58584, A5KUH7
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, Q, S, A, B, C, E, G, H, I | Designed riboflavin synthase (EC 2.5.1.9) | protein | 142 | 54% helix, 18% strand | Q58584 |
| M, O, D, F, J | Designed riboflavin synthase (EC 2.5.1.9) | protein | 141 | 55% helix, 18% strand | Q58584 |
| P, T, N, V, W, U, Y, Z, X, 2, 4, 1, L, R, 3 | Designed keto-hydroxyglutarate-ALDOLASE/KETO-deoxy- phosphogluconate aldolase (EC 4.1.3.16) | protein | 208 | 48% helix, 18% strand | A5KUH7 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.76 | 0.88 | 41 | empty |
| 2 | 281 | 0.76 | 0.87 | 40 | empty |
| 3 | 299 | 0.76 | 0.87 | 40 | empty |
| 4 | 312 | 0.70 | 0.83 | 43 | empty |
| 5 | 448 | 0.70 | 0.81 | 33 | empty |
Interfaces
39 interfaces between chains.
- O–S · 1084 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1078 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 1073 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1073 Ų buried · 16 hydrogen bonds · protein-protein
- K–S · 1071 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5IM5 · Crystal structure of designed two-component self-assembling icosahedral cage I53-40 · the same entry in another collection · chain B against B, 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 Q58584
- Every structure of UniProt A5KUH7
- Elsewhere: RCSB PDB 5IM5 · PDBe 5IM5 · UniProt Q58584 · UniProt A5KUH7
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