MolNFT v1 · #169345 · protein
Crystal structure of mbp-fused human APOBEC1
6X91 · Maltodextrin-binding protein, C->U-editing enzyme apobec-1…: “Crystal structure of mbp-fused human APOBEC1”. X-ray diffraction, 2 ligands (GLC, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #169345 on GenesisL1: 3D structure…
- PDB
- 6X91
- Type
- protein
- Length
- 4,667 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding protein, C->U-editing enzyme apobec-1 chimera
- EC
- 3.5.4.36
- UniProt
- A0A4Z0THX4, P41238
- Ligands
- GLC, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G | Maltodextrin-binding protein, C->U-editing enzyme apobec-1 chimera (EC 3.5.4.36) | protein | 592 | 42% helix, 19% strand | A0A4Z0THX4, P41238 |
| D | Maltodextrin-binding protein, C->U-editing enzyme apobec-1 chimera (EC 3.5.4.36) | protein | 557 | 43% helix, 15% strand | A0A4Z0THX4, P41238 |
| H | Maltodextrin-binding protein, C->U-editing enzyme apobec-1 chimera (EC 3.5.4.36) | protein | 558 | 45% helix, 15% strand | A0A4Z0THX4, P41238 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 28 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CAC · Cacodylate ion · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1179 | 0.86 | 0.87 | 103 | GLC |
| 2 | 1180 | 0.86 | 0.87 | 116 | GLC |
| 3 | 1047 | 0.80 | 0.81 | 134 | empty |
| 4 | 224 | 0.78 | 0.92 | 33 | empty |
| 5 | 225 | 0.77 | 0.91 | 35 | empty |
Interfaces
17 interfaces between chains.
- C–D · 1571 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1555 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1540 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1525 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 697 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 A0A4Z0THX4
- Every structure of UniProt P41238
- Elsewhere: RCSB PDB 6X91 · PDBe 6X91 · UniProt A0A4Z0THX4 · UniProt P41238
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