3QA3: A-domain

Crystal Structure of A-domain in complex with antibody. Determined by X-ray diffraction at 3.0 Å resolution. Released 30 Nov 2011.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Mus musculus, Homo sapiens
Chains: 12
Atoms: 19,772
Mol. weight: 282.01 kDa
Ligands: CA
Released: 30 Nov 2011

Explore 3QA3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QA3 contains 118 α-helices and 206 β-strands across 12 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: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	30-31	2	15
β-strand	36-37	2	15
β-strand	39-44	6	14
β-strand	51-55	5	14
β-strand	59-60	2	14
α-helix	61	1
β-strand	68-73	6	13
β-strand	76-81	6	13
α-helix	86-88	3
β-strand	91-96	6	14
α-helix	102	1
β-strand	103-104	2	14
β-strand	108-112	5	14
β-strand	117	1	16
β-strand	120-124	5	17
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-145	11	17
β-strand	146	1	16
β-strand	150-156	7	18
β-strand	159-160	2	18
β-strand	165-169	5	17
α-helix	170-173	4
β-strand	179-188	10	17
α-helix	189-193	5
β-strand	197-204	8	18
α-helix	210	1
β-strand	211-216	6	18

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	19
α-helix	9-11	3
β-strand	12-14	3	20
β-strand	20-26	7	19
α-helix	31-33	3
β-strand	34-41	8	20
β-strand	47-54	8	20
β-strand	59-62	4	20
α-helix	64-66	3
β-strand	70-75	6	19
β-strand	80-85	6	19
α-helix	90-92	3
β-strand	94-102	9	20
β-strand	111-114	4	20
β-strand	115	1	19
β-strand	118-122	5	20
β-strand	128	1	21
β-strand	131-135	5	22
β-strand	146-156	11	22
β-strand	157	1	21
β-strand	162-165	4	23
α-helix	166-168	3
β-strand	170	1	23
β-strand	174-182	9	22
β-strand	185-195	11	22
β-strand	205-210	6	23
α-helix	211-213	3
β-strand	215-220	6	23

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	30-31	2	3
β-strand	36-37	2	3
β-strand	39-44	6	2
β-strand	51-55	5	2
β-strand	59-60	2	2
α-helix	61	1
β-strand	68-73	6	1
β-strand	76-81	6	1
α-helix	86-88	3
β-strand	91-96	6	2
α-helix	102	1
β-strand	103-104	2	2
β-strand	108-112	5	2
β-strand	117	1	4
β-strand	120-124	5	5
α-helix	125-127	3
α-helix	128-133	6
β-strand	136-145	10	5
β-strand	146	1	4
β-strand	150-156	7	6
β-strand	159-160	2	6
α-helix	161	1
β-strand	167-169	3	5
α-helix	170-173	4
β-strand	179-187	9	5
α-helix	189-194	6
β-strand	197-204	8	6
α-helix	210	1
β-strand	211-216	6	6

Chain D: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	7
α-helix	9-11	3
β-strand	12-14	3	8
β-strand	20-26	7	7
α-helix	31-33	3
β-strand	34-41	8	8
β-strand	47-54	8	8
β-strand	59-62	4	8
α-helix	64-66	3
β-strand	70-75	6	7
α-helix	76-78	3
β-strand	80-85	6	7
α-helix	90-92	3
β-strand	94-102	9	8
β-strand	113-114	2	8
β-strand	115	1	7
β-strand	118-122	5	8
β-strand	128	1	9
β-strand	131-135	5	10
β-strand	146-156	11	10
β-strand	157	1	9
β-strand	162-165	4	11
α-helix	166-168	3
β-strand	170	1	11
β-strand	174-176	3	10
α-helix	177-179	3
β-strand	180-182	3	10
β-strand	185-195	11	10
β-strand	205-210	6	11
α-helix	211-213	3
β-strand	215-220	6	11

Chain E: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	133-140	8	24
α-helix	147-162	16
β-strand	169-176	8	24
β-strand	180-184	5	24
α-helix	186-191	6
α-helix	195-199	5
α-helix	211-217	7
α-helix	218-222	5
α-helix	225-227	3
α-helix	229-230	2
β-strand	234-241	8	24
α-helix	252-261	10
β-strand	264-271	8	24
α-helix	278-287	10
α-helix	289	1
α-helix	291	1
α-helix	292-295	4
β-strand	296-299	4	24
α-helix	303-305	3
α-helix	310-313	4

Chain F: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	10-13	4	26
β-strand	19-25	7	25
β-strand	30-31	2	27
β-strand	36-37	2	27
β-strand	39-44	6	26
β-strand	51-55	5	26
β-strand	59-60	2	26
α-helix	61	1
β-strand	68-73	6	25
β-strand	76-81	6	25
α-helix	86-88	3
β-strand	91-96	6	26
α-helix	102	1
β-strand	103-104	2	26
β-strand	108-112	5	26
β-strand	117	1	28
β-strand	120-124	5	29
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	29
β-strand	146	1	28
β-strand	150-156	7	30
β-strand	159-161	3	30
β-strand	165-169	5	29
α-helix	170-173	4
β-strand	179-188	10	29
α-helix	189-193	5
β-strand	197-204	8	30
α-helix	210	1
β-strand	211-216	6	30

Chain G: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	133-140	8	12
α-helix	147-162	16
β-strand	169-176	8	12
β-strand	180-184	5	12
α-helix	186-191	6
α-helix	195-199	5
α-helix	211-217	7
α-helix	218-222	5
α-helix	225-227	3
α-helix	229-230	2
β-strand	234-241	8	12
α-helix	252-261	10
β-strand	264-271	8	12
α-helix	273-275	3
α-helix	278-287	10
α-helix	289	1
α-helix	291	1
α-helix	292-295	4
β-strand	296-299	4	12
α-helix	305-308	4
α-helix	313-315	3

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	31
α-helix	9-11	3
β-strand	12-14	3	32
β-strand	20-26	7	31
α-helix	31-33	3
β-strand	34-41	8	32
β-strand	47-54	8	32
β-strand	59-62	4	32
α-helix	64-66	3
β-strand	70-75	6	31
β-strand	80-85	6	31
α-helix	90-92	3
β-strand	94-102	9	32
β-strand	113-114	2	32
β-strand	115	1	31
β-strand	118-122	5	32
β-strand	128	1	33
β-strand	131-135	5	34
β-strand	146-156	11	34
β-strand	157	1	33
β-strand	162-165	4	35
α-helix	166-168	3
β-strand	170	1	35
β-strand	174-176	3	34
α-helix	177-179	3
β-strand	180-182	3	34
β-strand	185-195	11	34
β-strand	205-210	6	35
α-helix	211-213	3
β-strand	215-220	6	35
α-helix	223-225	3

4 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
Antibody Light chain	A, C, F, J	protein	220	Mus musculus
Antibody Heavy chain	B, D, H, K	protein	224	Mus musculus
Integrin alpha-M	E, G, I, L	protein	190	Homo sapiens	P11215 (AlphaFold model)

Sequence of entity 1 (A, C, F, J), FASTA

>3QA3_1 Antibody Light chain (chains A, C, F, J)
DIEMTQSPSSLGVSVGEKVTMSCKSSQNLLYSSNQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGTGSGTDFTLTISSVKAEDLAVYYCQQYYSYPLTFGAGTKLELKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, D, H, K), FASTA

>3QA3_2 Antibody Heavy chain (chains B, D, H, K)
QVQLQQSGAELVKPGASVKLSCTPSGFNIKDIYMQWVKQRPEQGLEWIGRIDPANDKTKY
DPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCASEGHYGYDGYAMDYWGQGTTVTV
SSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (E, G, I, L), FASTA

>3QA3_3 Integrin alpha-M (chains E, G, I, L)
DSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQN
NPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITNGARKNAFKILVVITDGEKFGDPLG
YEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQ
LREKGFAIEG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

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

Primary citation

Stable Coordination of the Inhibitory Ca2+ Ion at the Metal Ion-Dependent Adhesion Site in Integrin CD11b/CD18 by an Antibody-Derived Ligand Aspartate: Implications for Integrin Regulation and Structure-Based Drug Design. Mahalingam, B., Ajroud, K., Alonso, J.L. et al. J Immunol (2011) 187:6393-6401. DOI 10.4049/jimmunol.1102394 · PubMed

Other PDB entries of the same protein (UniProt P11215 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MF7 1.25 Å, Integrin alpha M I domain
1NA5 1.5 Å, Integrin alpha M I domain
8CE6 1.58 Å, Crystal structure of human Cd11b I domain in P212121 space group
1IDO 1.7 Å, I-domain from integrin CR3, MG2+ bound
1JLM 2.0 Å, I-domain from integrin CR3, MN2+ bound
4XW2 2.0 Å, Structural basis for simvastatin competitive antagonism of complement receptor 3
8CE9 2.11 Å, Crystal structure of human Cd11b I domain in C121 space group
1M1U 2.3 Å, An isoleucine-based allosteric switch controls affinity and shape shifting in integrin…
1N9Z 2.5 Å, Integrin alpha M I domain mutant
9RM9 2.6 Å, Cryo-EM structure of alphaM/beta2 headpiece complex without alphaM I-domain - the…
1BHO 2.7 Å, Mac-1 I domain magnesium complex
1BHQ 2.7 Å, Mac-1 I domain cadmium complex

Browse structure collections

About this viewer

MolViewer shows 3QA3 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.