MolNFT v1 · #109921 · protein

Crystal structure of human paxillin LD4 motif in complex with Fab fragment

4XH2 · Fab heavy chain: “Crystal structure of human paxillin LD4 motif in complex with Fab fragment”. X-ray diffraction, 2 ligands (ACE, PO4), 20 pockets (best druggability 0.86). MolNFT v1 #109921 on GenesisL1: 3D structure, binding sites…

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.

Pocket	Volume (Å³)	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 Å² buried · 14 hydrogen bonds · protein-protein
G–I · 2155 Å² buried · 17 hydrogen bonds · protein-protein
J–K · 2153 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 2050 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1997 Å² 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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