MolNFT v1 · #158600 · protein
Crystal structure of computationally designed protein XXA_GVDQ
6NZ1 · Design construct XXA_GVDQ: “Crystal structure of computationally designed protein XXA_GVDQ”. X-ray diffraction, 8 pockets (best druggability 0.50). MolNFT v1 #158600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NZ1
- Type
- protein
- Length
- 569 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Design construct XXA_GVDQ
- Pockets
- 8 · best druggability 0.50
Structure
x-ray diffraction · 5 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Design construct XXA_GVDQ | protein | 92 | 87% helix, 0% strand | — |
| B, E | Design construct XXA_GVDQ | protein | 97 | 85% helix, 0% strand | — |
| C | Design construct XXA_GVDQ | protein | 94 | 87% helix, 0% strand | — |
| D | Design construct XXA_GVDQ | protein | 94 | 88% helix, 0% strand | — |
| F | Design construct XXA_GVDQ | protein | 95 | 85% helix, 0% strand | — |
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.50 | 0.84 | 18 | empty |
| 2 | 227 | 0.48 | 0.74 | 30 | empty |
| 3 | 181 | 0.48 | 0.76 | 27 | empty |
| 4 | 155 | 0.43 | 0.75 | 23 | empty |
| 5 | 81 | 0.41 | 0.79 | 17 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1605 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1591 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1575 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1549 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1432 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6NZ1 · Crystal structure of computationally designed protein XXA_GVDQ · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6NZ1 · PDBe 6NZ1
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