Research workbench
Crystal structure of human paxillin LD4 motif in complex with Fab fragment
Analyse Crystal structure of human paxillin LD4 motif in complex with Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XH2
- Type
- protein
- Length
- 2,654 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain; Fab light chain; Paxillin LD4
- Ligands
- ACE, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 15 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Fab heavy chain | protein | 220 | 6% helix, 50% strand | — |
| B, D | Fab light chain | protein | 210 | 6% helix, 51% strand | — |
| C | Fab heavy chain | protein | 220 | 7% helix, 52% strand | — |
| E | Fab heavy chain | protein | 220 | 7% helix, 50% strand | — |
| F | Fab light chain | protein | 209 | 5% helix, 52% strand | — |
| H | Fab heavy chain | protein | 213 | 6% helix, 52% strand | — |
| I, L | Fab light chain | protein | 209 | 6% helix, 51% strand | — |
| J | Fab heavy chain | protein | 222 | 7% helix, 52% strand | — |
| K | Fab light chain | protein | 210 | 6% helix, 51% strand | — |
| a | Paxillin LD4 | protein | 16 | 69% helix, 0% strand | — |
| c | Paxillin LD4 | protein | 11 | 73% helix, 0% strand | — |
| e | Paxillin LD4 | protein | 17 | 76% helix, 0% strand | — |
| g | Paxillin LD4 | protein | 14 | 57% helix, 0% strand | — |
| h | Paxillin LD4 | protein | 12 | 67% helix, 0% strand | — |
| j | Paxillin LD4 | protein | 12 | 58% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains J, L
- PO4 · Phosphate ion · ion · 2 copies · chains C, D, E, F
- GOL · Glycerol · additive · 20 copies · chains A, B, C, D, E, F, K, G, H, L, I, J
- ACT · Acetate ion · additive · chains F, K
- LDA · Lauryl dimethylamine-N-oxide · additive · chains F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.86 | 0.87 | 144 | GOL |
| 2 | 831 | 0.75 | 0.79 | 106 | empty |
| 3 | 668 | 0.74 | 0.80 | 109 | GOL |
| 4 | 251 | 0.67 | 0.84 | 31 | empty |
| 5 | 588 | 0.65 | 0.76 | 59 | empty |
Interfaces
32 interfaces between chains.
- C–D · 2163 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 2155 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 2153 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2050 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1997 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide (disulfide).
Compared structures
- 4XH2 · Crystal structure of human paxillin LD4 motif in complex with Fab fragment · 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 4XH2 · PDBe 4XH2
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