4ZFG: Dual-specificity Fab 5A12

Dual-specificity Fab 5A12 in complex with Angiopoietin 2. Determined by X-ray diffraction at 2.27 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,445
Mol. weight: 74.48 kDa
Ligands: CA
Released: 1 Jul 2015

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

Secondary structure: helices and β-sheets

4ZFG contains 25 α-helices and 59 β-strands across 3 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: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	284-289	6
β-strand	296-301	6	1
β-strand	308-314	7	1
α-helix	317-319	3
β-strand	322-328	7	1
α-helix	339-344	6
β-strand	346-347	2	1
β-strand	353-354	2	1
α-helix	357-366	10
β-strand	369-376	8	1
β-strand	382-392	11	1
α-helix	395-397	3
β-strand	401-408	8	1
α-helix	421-423	3
β-strand	424	1	2
β-strand	425	1	3
β-strand	428	1	3
α-helix	437-441	5
β-strand	445	1	2
β-strand	453-454	2	4
β-strand	473-474	2	4
α-helix	475-478	4
α-helix	482-484	3
β-strand	486-493	8	1

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	10-12	3	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	33-39	7	6
β-strand	46-52	7	6
β-strand	56-59	4	6
β-strand	67-72	6	5
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	88-95	8	6
β-strand	100C-103	4	6
β-strand	107-111	5	6
α-helix	115-116	2
β-strand	117	1	7
β-strand	120-124	5	8
β-strand	135-145	11	8
β-strand	146	1	7
β-strand	151-154	4	9
α-helix	155-157	3
β-strand	159	1	9
β-strand	163-165	3	8
α-helix	166-168	3
β-strand	169-170	2	8
β-strand	176-185	10	8
β-strand	189	1	10
β-strand	192	1	10
β-strand	195-200	6	9
α-helix	201-203	3
β-strand	205-210	6	9

Chain L: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-14	5	12
β-strand	19-28	11	11
α-helix	30-32	3
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-75	14	11
α-helix	80-82	3
β-strand	84-90	7	12
α-helix	97	1
β-strand	98	1	12
α-helix	99	1
β-strand	102-107	6	12
β-strand	111	1	13
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
α-helix	155	1
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-187	5
β-strand	191-197	7	15
β-strand	205-210	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Angiopoietin-2	A	protein	232	Homo sapiens	O15123 (AlphaFold model)
Fragment antigen binding 5A12 heavy chain	H	protein	228	Homo sapiens
Fragment antigen binding 5A12 light chain	L	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>4ZFG_1 Angiopoietin-2 (chains A)
AGSEQISFRDCAEVFKSGHTTNGIYTLTFPNSTEEIKAYCDMEAGGGGWTIIQRREDGSV
DFQRTWKEYKVGFGNPSGEYWLGNEFVSQLTNQQRYVLKIHLKDWEGNEAYSLYEHFYLS
SEELNYRIHLKGLTGTAGKISSISQPGNDFSTKDGDNDKCICKCSQMLTGGWWFDACGPS
NLNGMYYPQRQNTNKFNGIKWYYWKGSGYSLKATTMMIRPADFGNSHHHHHH

Sequence of entity 2 (H), FASTA

>4ZFG_2 Fragment antigen binding 5A12 heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (L), FASTA

>4ZFG_3 Fragment antigen binding 5A12 light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQFLSSFGVAWYQQKPGKAPKLLIYGASSLYSGVP
SRFSGSGSGTDFTLTISSLQPEDFATYYCQQGLLSPLTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Deep Sequencing-guided Design of a High Affinity Dual Specificity Antibody to Target Two Angiogenic Factors in Neovascular Age-related Macular Degeneration. Koenig, P., Lee, C.V., Sanowar, S. et al. J Biol Chem (2015) 290:21773-21786. DOI 10.1074/jbc.M115.662783 · PubMed

Other PDB entries of the same protein (UniProt O15123 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JZC 1.9 Å, Angiopoietin-2 fibrinogen domain TAG mutant
1Z3U 2.25 Å, Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces…
1Z3S 2.35 Å, Angiopoietin-2 Receptor Binding Domain
8VGP 2.7 Å, CryoEM structure of Angiopoietin-2 in complex with engineered conformationally rigid Fab…
9HMI 2.87 Å, Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2…
2GY7 3.7 Å, Angiopoietin-2/Tie2 Complex Crystal Structure

Browse structure collections

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