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Crystal structure of human paxillin LD2 motif in complex with Fab fragment

Analyse Crystal structure of human paxillin LD2 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: 4XGZ
Type: protein
Length: 5,303 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; Paxillin LD2
Ligands: NO3
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 19 distinct chains · 10% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab heavy chain	protein	217	10% helix, 53% strand	—
B, D, K, N, P, T, V, X	Fab light chain	protein	210	7% helix, 52% strand	—
C	Fab heavy chain	protein	219	9% helix, 53% strand	—
E	Fab heavy chain	protein	212	8% helix, 55% strand	—
F	Fab light chain	protein	207	7% helix, 53% strand	—
G, W	Fab heavy chain	protein	218	9% helix, 53% strand	—
H	Fab heavy chain	protein	219	9% helix, 53% strand	—
I, R	Fab light chain	protein	211	7% helix, 52% strand	—
J	Fab heavy chain	protein	224	8% helix, 52% strand	—
L	Fab light chain	protein	209	7% helix, 52% strand	—
M	Fab heavy chain	protein	220	9% helix, 53% strand	—
O	Fab heavy chain	protein	223	9% helix, 52% strand	—
Q	Fab heavy chain	protein	217	9% helix, 53% strand	—
S	Fab heavy chain	protein	215	9% helix, 53% strand	—
U	Fab heavy chain	protein	217	9% helix, 55% strand	—
a, h, o, s, w	Paxillin LD2	protein	12	83% helix, 0% strand	—
c	Paxillin LD2	protein	16	88% helix, 0% strand	—
e, g, m, u	Paxillin LD2	protein	13	85% helix, 0% strand	—
j, q	Paxillin LD2	protein	19	68% helix, 0% strand	—

Ligands and binding sites

NO3 · Nitrate ion · ion · 12 copies · chains B, D, F, I, K, L, N, P, R, T, V, X
EDO · 1,2-ethanediol · additive · 3 copies · chains N, Q, W

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1195	0.85	0.86	162	empty
2	795	0.79	0.83	95	EDO
3	900	0.79	0.82	89	empty
4	1075	0.77	0.80	121	empty
5	722	0.75	0.80	81	empty

Interfaces

87 interfaces between chains.

O–P · 2016 Å² buried · 17 hydrogen bonds · protein-protein
H–L · 1969 Å² buried · 15 hydrogen bonds · protein-protein
W–X · 1964 Å² buried · 16 hydrogen bonds · protein-protein
J–K · 1951 Å² buried · 13 hydrogen bonds · protein-protein
U–V · 1945 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 57 disulfide (disulfide).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4XGZ · PDBe 4XGZ

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