6W00: Fab239

Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein. Determined by X-ray diffraction at 1.85 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Streptococcus sp. group G, Homo sapiens, Plasmodium falciparum
Chains: 4
Atoms: 4,174
Mol. weight: 54.98 kDa
Released: 29 Jul 2020

Explore 6W00 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W00 contains 19 α-helices and 48 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 G: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	1
β-strand	17-25	9	1
α-helix	28-41	14
β-strand	47-51	5	1
β-strand	56-60	5	1

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-59	3	8
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	100D-103	4	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	128-130	3
β-strand	131-132	2	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	1
α-helix	155-157	3
β-strand	159	1	1
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	195-200	6	1
α-helix	201-203	3
β-strand	205-210	6	1
α-helix	212-214	3

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	2
β-strand	10-13	4	3
β-strand	19-25	7	2
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	85-90	6	3
β-strand	98	1	3
β-strand	102-106	5	3
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-197	7	6
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G-binding protein G	G	protein	58	Streptococcus sp. group G	P19909 (AlphaFold model)
Fab239 light chain	L	protein	215	Homo sapiens
Fab239 heavy chain	H	protein	224	Homo sapiens
NPNA2 peptide	P	protein	9	Plasmodium falciparum	P02893 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>6W00_1 Immunoglobulin G-binding protein G (chains G)
AVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTE

Sequence of entity 2 (L), FASTA

>6W00_2 Fab239 light chain (chains L)
DIQMTQSPSTLSASVGDRVTITCRASQSVSTSLAWYQQKPGKAPNLLIYQASTLYRGVPS
RFSGSGSGTEFTLTIGSLQPDDFATYYCQHYNSYSRITFGQGTRLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>6W00_3 Fab239 heavy chain (chains H)
QVQLVESGGGVVQPGRSLRLSCAASRLTFRNFGMHWVRQTPGKGLEWVAVIWHDGSNKFY
ADSVEGRFTISRDNSKNTLYLQMNSLRDEDTAIYYCAKDWGGASDRVFDYWGRGTLVIVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 4 (P), FASTA

>6W00_4 NPNA2 peptide (chains P)
XNPNANPNA

Primary citation

Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum. Pholcharee, T., Oyen, D., Flores-Garcia, Y. et al. Nat Commun (2021) 12:1063-1063. DOI 10.1038/s41467-021-21221-4 · PubMed

Other PDB entries of the same protein (UniProt P19909 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FIL 0.88 Å, Structural and energetic determinants for hyperstable variants of GB1 obtained from…
2QMT 1.05 Å, Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR and X-ray Diffraction
9I2I 1.08 Å, X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and…
6CHE 1.1 Å, Selenomethionine mutant (A34Sem) of protein GB1 examined by X-ray diffraction
6CPZ 1.12 Å, Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction
2GI9 1.14 Å, Backbone Conformational Constraints in a Microcrystalline U-15N-Labeled Protein by 3D…
6C9O 1.2 Å, Selenomethionine mutant (V29Sem) of protein GB1 examined by X-ray diffraction
6CTE 1.2 Å, 77Se-NMR probes the protein environment of selenomethionine
6OC7 1.3 Å, HMP42 Fab in complex with Protein G
6NLA 1.34 Å, Crystal structure of de novo designed metal-controlled dimer of B1…
2ON8 1.35 Å, Gbeta1 stabilization by in vitro evolution and computational design
12LO 1.37 Å, X-ray crystal structure of Protein GB1 mutant K13A

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