MolNFT v1 · #98081 · protein
Crystal structure of the phospholipase vipd from legionella pneumophila in complex with the human GTPase RAB5
4KYI: “Crystal structure of the phospholipase vipd from legionella pneumophila in complex with the human GTPase RAB5”. X-ray diffraction, 2 ligands (GNP, MG), 20 pockets (best druggability 0.76). MolNFT v1 #98081 on GenesisL1: 3D…
- 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
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