Research workbench
Coping with strong translational non-crystallographic symmetry and extreme anisotropy in molecular replacement with phaser: human RAB27A
Analyse Coping with strong translational non-crystallographic symmetry and extreme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HUF
- Type
- protein
- Length
- 2,736 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-27A
- UniProt
- P51159
- Ligands
- GNP, MG
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O, N, B, E, C, K, M, D, P, F, J, G, I, H, L | RAS-related protein rab-27A | protein | 171 | 37% helix, 21% strand | P51159 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 16 copies · chains A, O, N, B, E, C, K, M, D, P, F, J, G, I, H, L
- MG · Magnesium ion · metal · 16 copies · chains A, O, N, B, E, C, K, M, D, P, F, J, G, I, H, L
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 | 546 | 0.66 | 0.77 | 65 | MG, GNP |
| 2 | 535 | 0.66 | 0.77 | 66 | MG, GNP |
| 3 | 567 | 0.66 | 0.77 | 66 | MG, GNP |
| 4 | 529 | 0.66 | 0.77 | 65 | MG, GNP |
| 5 | 529 | 0.66 | 0.77 | 63 | MG, GNP |
Interfaces
24 interfaces between chains.
- A–E · 321 Ų buried · 9 hydrogen bonds · protein-protein
- O–K · 320 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 318 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 316 Ų buried · 8 hydrogen bonds · protein-protein
- P–L · 311 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6HUF · Coping with strong translational non-crystallographic symmetry and extreme anisotropy in… · the same entry in another collection · chain L against L, 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 P51159
- Elsewhere: RCSB PDB 6HUF · PDBe 6HUF · UniProt P51159
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