2B2X: VLA1 RdeltaH I-domain

VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab. Determined by X-ray diffraction at 2.2 Å resolution. Released 18 Apr 2006.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Rattus norvegicus, Mus musculus
Chains: 6
Atoms: 9,537
Mol. weight: 145.64 kDa
Ligands: MG
Released: 18 Apr 2006

Explore 2B2X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2B2X contains 55 α-helices and 98 β-strands across 6 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: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	147-154	8	1
α-helix	162-173	12
β-strand	185-190	6	1
β-strand	194-198	5	1
α-helix	206-213	8
α-helix	216-218	3
α-helix	226-232	7
α-helix	233-237	5
α-helix	240-242	3
α-helix	244-245	2
β-strand	249-256	8	1
α-helix	263-265	3
α-helix	266-274	9
β-strand	278-285	8	1
α-helix	287-289	3
α-helix	297-304	8
α-helix	308	1
α-helix	311-313	3
β-strand	315-318	4	1
α-helix	323-327	5
α-helix	328-332	5

Chain B: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	148-154	7	12
α-helix	162-172	11
β-strand	184-190	7	12
β-strand	194-198	5	12
α-helix	208-213	6
α-helix	216-218	3
α-helix	226-232	7
α-helix	233-237	5
α-helix	240-242	3
β-strand	251-256	6	12
α-helix	263-265	3
α-helix	266-275	10
β-strand	279-285	7	12
α-helix	297-304	8
α-helix	308	1
β-strand	315-318	4	12
α-helix	321-327	7
α-helix	328-335	8

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	2
β-strand	10-12	3	3
β-strand	18-25	8	2
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
β-strand	64	1	2
β-strand	67-72	6	2
β-strand	77-82	6	2
α-helix	87-89	3
β-strand	91-99	9	3
β-strand	104-108	5	3
β-strand	112-116	5	3
α-helix	119-121	3
β-strand	122	1	4
β-strand	125-129	5	5
β-strand	140-150	11	5
β-strand	151	1	4
β-strand	156-159	4	6
α-helix	160-162	3
β-strand	168-170	3	5
α-helix	171-173	3
β-strand	174-176	3	5
β-strand	179-189	11	5
β-strand	199-204	6	6
α-helix	205-207	3
β-strand	209-214	6	6

Chain I: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-51	7	14
β-strand	57-59	3	14
α-helix	61-63	3
β-strand	64	1	13
β-strand	67-72	6	13
β-strand	77-82	6	13
α-helix	87-89	3
β-strand	91-99	9	14
β-strand	104-108	5	14
β-strand	112-116	5	14
α-helix	119-121	3
β-strand	122	1	15
β-strand	125-129	5	16
β-strand	140-150	11	16
β-strand	151	1	15
β-strand	156-159	4	17
α-helix	160-162	3
β-strand	168-170	3	16
α-helix	171-173	3
β-strand	174-176	3	16
β-strand	179-189	11	16
α-helix	190-192	3
β-strand	199-204	6	17
α-helix	205-207	3
β-strand	209-214	6	17

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-37	5	8
β-strand	44-48	5	8
β-strand	52-53	2	8
α-helix	54	1
β-strand	61-66	6	7
β-strand	69-74	6	7
α-helix	79-81	3
β-strand	83-89	7	8
α-helix	95	1
β-strand	96-97	2	8
β-strand	101-105	5	8
β-strand	115	1	9
α-helix	116-117	2
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	10
β-strand	144	1	9
β-strand	149-154	6	11
β-strand	157-159	3	11
β-strand	163-167	5	10
β-strand	177-186	10	10
α-helix	187-192	6
β-strand	196-201	6	11
α-helix	208	1
β-strand	209-213	5	11

Chain M: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-25	7	18
β-strand	33-37	5	19
β-strand	44-48	5	19
β-strand	52-53	2	19
α-helix	54	1
β-strand	61-66	6	18
β-strand	69-74	6	18
α-helix	79-81	3
β-strand	83-89	7	19
α-helix	95	1
β-strand	96-97	2	19
β-strand	101-105	5	19
β-strand	115	1	20
β-strand	118-122	5	21
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	21
β-strand	144	1	20
β-strand	149-154	6	22
β-strand	158-159	2	22
β-strand	163-167	5	21
β-strand	177-186	10	21
α-helix	187-192	6
β-strand	195-201	7	22
β-strand	209-214	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-1	A, B	protein	223	Rattus norvegicus	P18614 (AlphaFold model)
Antibody AQC2 Fab	H, I	protein	226	Mus musculus	P01868 (AlphaFold model)
Antibody AQC2 Fab	L, M	protein	213	Mus musculus

Sequence of entity 1 (A, B), FASTA

>2B2X_1 Integrin alpha-1 (chains A, B)
GSVSPTFQVVNSFAPVQECSTQLDIVIVLDGSNSIYPWESVIAFLNDLLKRMDIGPKQTQ
VGIVQYGENVTHEFNLNKYSSTEEVLVAANKIVQRGGRQTMTALGIDTARKEAFTEARGA
RRGVKKVMVIVTDGESHDNYRLKQVIQDCEDENIQRFSIAILGHYNRGNLSTEKFVEEIK
SIASEPTEKHFFNVSDELALVTIVKALGERIFALEALERPHRD

Sequence of entity 2 (H, I), FASTA

>2B2X_2 Antibody AQC2 Fab (chains H, I)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSRYTMSWVRQAPGKGLEWVAVISGGGHTYYL
DSVEGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCTRGFGDGGYFDVWGQGTLVTVSSAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCHHHHHH

Sequence of entity 3 (L, M), FASTA

>2B2X_3 Antibody AQC2 Fab (chains L, M)
QIQLTQSPSSLSASVGDRVTITCSASSQVNHMFWYQQKPGKAPKPWIYLTSYLASGVPSR
FSGSGSGTDYTLTISSLQPEDFATYYCQQWSGNPWTFGQGTKVEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design. Clark, L.A., Boriack-Sjodin, P.A., Eldredge, J. et al. Protein Sci (2006) 15:949-960. DOI 10.1110/ps.052030506 · PubMed

Other PDB entries of the same protein (UniProt P18614 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1CK4 2.2 Å, Crystal structure of rat A1B1 integrin I-domain.
1MHP 2.8 Å, Crystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab…

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