Research workbench
Crystal structure of the phospholipase vipd from legionella pneumophila in complex with the human GTPase RAB5
Analyse Crystal structure of the phospholipase vipd from legionella pneumophila in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KYI
- Type
- protein
- Length
- 2,772 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vipd; RAS-related protein rab-5C
- UniProt
- Q5ZRP9, P51148
- Ligands
- GNP, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vipd | protein | 530 | 47% helix, 11% strand | Q5ZRP9 |
| B, D, F, H | RAS-related protein rab-5C | protein | 164 | 37% helix, 29% strand | P51148 |
| C | Vipd | protein | 527 | 47% helix, 11% strand | Q5ZRP9 |
| E | Vipd | protein | 531 | 48% helix, 11% strand | Q5ZRP9 |
| G | Vipd | protein | 528 | 47% helix, 10% strand | Q5ZRP9 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains B, D, F, H
- MG · Magnesium ion · metal · 4 copies · chains B, D, F, H
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, E, G
- GOL · Glycerol · additive · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.76 | 0.91 | 33 | empty |
| 2 | 288 | 0.75 | 0.88 | 37 | empty |
| 3 | 912 | 0.74 | 0.78 | 86 | GOL |
| 4 | 383 | 0.74 | 0.84 | 39 | empty |
| 5 | 271 | 0.72 | 0.86 | 37 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1025 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 979 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 949 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 897 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 889 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4KYI · Crystal structure of the phospholipase VipD from Legionella pneumophila in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
- P51148 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-5C (P51148) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q5ZRP9
- Every structure of UniProt P51148
- Elsewhere: RCSB PDB 4KYI · PDBe 4KYI · UniProt Q5ZRP9 · UniProt P51148
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.