6OC7: HMP42 Fab

HMP42 Fab in complex with Protein G. Determined by X-ray diffraction at 1.3 Å resolution. Released 5 Feb 2020.

Method: X-ray diffraction
Resolution: 1.3 Å
Organisms: Homo sapiens, Streptococcus sp. group G
Chains: 3
Atoms: 4,473
Mol. weight: 55.32 kDa
Released: 5 Feb 2020

Explore 6OC7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OC7 contains 18 α-helices and 49 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 C: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	1-8	8	5
β-strand	12-20	9	5
α-helix	23-36	14
β-strand	42-46	5	5
β-strand	51-55	5	5

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	100-103	4	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-128	9	4
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	186-188	3
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	6
β-strand	9-13	4	7
β-strand	19-24	6	6
α-helix	28-30	3
β-strand	34-38	5	7
β-strand	45-48	4	7
β-strand	49	1	8
β-strand	53	1	8
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-91	8	7
β-strand	96-98	3	7
β-strand	102-106	5	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-155	3	11
β-strand	159-161	3	10
α-helix	162-164	3
β-strand	165-166	2	10
β-strand	172-180	9	10
α-helix	182-187	6
β-strand	191-197	7	11
β-strand	200-206	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of HMP42 Fab	H	protein	231	Homo sapiens
Light chain for HMP42 Fab	L	protein	214	Homo sapiens
Immunoglobulin G-binding protein G	C	protein	66	Streptococcus sp. group G	P19909 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6OC7_1 Heavy chain of HMP42 Fab (chains H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNY
AQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARDRGREWELESYYYYYYMDVWGK
GTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>6OC7_2 Light chain for HMP42 Fab (chains L)
SYELTQPPSVSVSPGQTARITCSGDALPKQYAYWYQQKPGQAPVLVIYKDSERPSGIPER
FSGSSSGTTVTLTISGVQAEDEADYYCQSADSSGTYVVFGGGTKLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (C), FASTA

>6OC7_3 Immunoglobulin G-binding protein G (chains C)
MTPAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVT
EHHHHH

Primary citation

A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Steichen, J.M., Lin, Y.C., Havenar-Daughton, C. et al. Science (2019) 366. DOI 10.1126/science.aax4380 · 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
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
6NL6 1.4 Å, Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G…

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