4XH2: Human paxillin LD4 motif

Crystal structure of human paxillin LD4 motif in complex with Fab fragment. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 18
Atoms: 21,729
Mol. weight: 301.9 kDa
Ligands: PO4, LDA, ACE
Released: 1 Jul 2015

Explore 4XH2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XH2 contains 106 α-helices and 256 β-strands across 18 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain a: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11

Chain A: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	100A-103	4	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	125-127	3
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-190	5
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain B: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	9-13	5	6
β-strand	18-22	5	7
β-strand	32-38	7	6
β-strand	45-49	5	6
β-strand	53-54	2	6
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-91	7	6
β-strand	96-98	3	6
α-helix	99-101	3
β-strand	102-106	5	6
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-156	4	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
β-strand	205-210	6	10

Chains c and h: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8

Chain C: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	18-25	8	11
β-strand	34-39	6	13
β-strand	45-52	8	13
β-strand	56-59	4	13
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	100A-103	4	13
β-strand	107-109	3	13
β-strand	110-111	2	12
α-helix	114-116	3
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-124	5	15
α-helix	125-126	2
β-strand	127	1	16
α-helix	129-131	3
β-strand	135-145	11	15
β-strand	146	1	14
β-strand	151-154	4	17
α-helix	155-157	3
β-strand	159	1	17
β-strand	163-165	3	15
α-helix	166-168	3
β-strand	169-170	2	15
β-strand	176-185	10	15
α-helix	186-188	3
β-strand	195-200	6	17
α-helix	201-203	3
β-strand	205-210	6	17
β-strand	214	1	16

Chain D: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	9-13	5	18
β-strand	18-22	5	10
β-strand	32-38	7	18
β-strand	45-49	5	18
β-strand	53-54	2	18
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	85-91	7	18
β-strand	96-98	3	18
α-helix	99-101	3
β-strand	102-106	5	18
β-strand	111	1	19
α-helix	112-113	2
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	144-150	7	7
β-strand	153-156	4	7
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	191-198	8	7
β-strand	205-210	6	7

Chain e: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13

Chain E: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	34-39	6	22
β-strand	45-51	7	22
β-strand	57-59	3	22
β-strand	67-72	6	21
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-95	8	22
β-strand	100A-103	4	22
β-strand	107-111	5	22
α-helix	114-116	3
β-strand	117	1	23
α-helix	118-119	2
β-strand	120-124	5	24
β-strand	135-145	11	24
β-strand	146	1	23
β-strand	151-154	4	25
α-helix	155-157	3
β-strand	159	1	25
β-strand	164-165	2	24
α-helix	166-168	3
β-strand	169-170	2	24
β-strand	176-185	10	24
α-helix	188-191	4
β-strand	192	1	26
β-strand	195-200	6	25
α-helix	201-203	3
β-strand	205-210	6	25

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab Heavy Chain	A, C, E, G, H, J	protein	228	Homo sapiens
Fab Light Chain	B, D, F, I, K, L	protein	217	Homo sapiens
paxillin LD4	a, c, e, g, h, j	protein	18	synthetic construct	P49023 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, H, J), FASTA

>4XH2_1 Fab Heavy Chain (chains A, C, E, G, H, J)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSSYSIHWVRQAPGKGLEWVAYISSSSGY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARTWYYGFDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (B, D, F, I, K, L), FASTA

>4XH2_2 Fab Light Chain (chains B, D, F, I, K, L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQFKRQKEPITFGQGTKVEIKRTVAAPSVFI
FPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (a, c, e, g, h, j), FASTA

>4XH2_3 paxillin LD4 (chains a, c, e, g, h, j)
WGGSATRELDELMASLSD

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	1
ACE	Acetyl group	C2 H4 O	2

Water and common crystallization additives (GOL, ACT) are not listed.

Primary citation

Engineering Synthetic Antibody Inhibitors Specific for LD2 or LD4 Motifs of Paxillin. Nocula-Lugowska, M., Lugowski, M., Salgia, R. et al. J Mol Biol (2015) 427:2532-2547. DOI 10.1016/j.jmb.2015.06.004 · PubMed

Other PDB entries of the same protein (UniProt P49023 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2O9V 1.63 Å, The second SH3 domain from Ponsin in complex with the paxillin proline rich region
2VZG 1.8 Å, Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex…
6PW8 1.95 Å, Hydrocarbon-Stapled Paxillin Peptide Bound to the Focal Adhesion Targeting (FAT) Domain…
2VZD 2.1 Å, Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex…
2VZI 2.2 Å, Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex…
5UWH 2.26 Å, Crystal Structure of Paxillin NES Peptide in complex with CRM1-Ran-RanBP1
1OW6 2.35 Å, Paxillin LD4 motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal…
3RQG 2.5 Å, Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD4
4XGZ 2.5 Å, Crystal structure of human paxillin LD2 motif in complex with Fab fragment
9QWO 2.54 Å, Vinculin tail bound to paxillin LD2
1OW7 2.6 Å, Paxillin LD4 motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal…
6IUI 2.6 Å, Crystal structure of GIT1 PBD domain in complex with Paxillin LD4 motif

Browse structure collections

About this viewer

MolViewer shows 4XH2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.