4YR6: Fab fragment of 5G6

Fab fragment of 5G6 in complex with epitope peptide. Determined by X-ray diffraction at 2.38 Å resolution. Released 9 Mar 2016.

Method: X-ray diffraction
Resolution: 2.38 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 6,914
Mol. weight: 96.99 kDa
Released: 9 Mar 2016

Explore 4YR6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YR6 contains 33 α-helices and 87 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: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
α-helix	17	1
β-strand	18-25	8	1
β-strand	34-41	8	3
β-strand	48-54	7	3
β-strand	59-61	3	3
α-helix	63-66	4
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-103	11	3
β-strand	106-112	7	3
β-strand	116-118	3	3
β-strand	119-120	2	2
β-strand	126	1	4
α-helix	127-128	2
β-strand	129-133	5	5
β-strand	144-154	11	5
β-strand	155	1	4
β-strand	160-163	4	6
α-helix	164-166	3
β-strand	168	1	6
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	184-193	10	5
α-helix	196-199	4
β-strand	203-208	6	6
α-helix	209-211	3
β-strand	213-218	6	6

Chain B: 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	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	98	1	8
β-strand	102-106	5	8
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-155	3	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-197	7	11
α-helix	204	1
β-strand	205-210	6	11

Chains C and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain D: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
α-helix	17	1
β-strand	18-25	8	12
β-strand	34-41	8	14
β-strand	48-54	7	14
β-strand	59-61	3	14
α-helix	66-68	3
β-strand	69-74	6	12
β-strand	79-84	6	12
α-helix	89-91	3
β-strand	93-103	11	14
β-strand	106-112	7	14
β-strand	116-118	3	14
β-strand	119-120	2	13
β-strand	126	1	15
β-strand	129-133	5	16
β-strand	145-154	10	16
β-strand	155	1	15
β-strand	160-163	4	17
α-helix	164-166	3
β-strand	172-174	3	16
α-helix	175-177	3
β-strand	178-180	3	16
β-strand	183-192	10	16
α-helix	196-199	4
β-strand	203-208	6	17
α-helix	209-211	3
β-strand	213-218	6	17

Chain E: 8 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	33-38	6	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-90	7	19
α-helix	96	1
β-strand	98	1	19
β-strand	102-106	5	19
β-strand	111	1	20
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	154-155	2	22
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	185-188	4
β-strand	191-197	7	22
α-helix	204	1
β-strand	205-210	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain of 5G6	A, D	protein	221	Mus musculus
light chain of 5G6	B, E	protein	214	Mus musculus
Ace-lys-leu-arg-gly-val-leu-gln-gly-his-leu	C, F	protein	11	Homo sapiens	P07359 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4YR6_1 heavy chain of 5G6 (chains A, D)
QVTLKESGPGILQPSQTLSLTCSFSGFSLSTSNMGVVWIRQPSGKGLEWLLHILWNDGKF
YNPALKSRLTISKDTYNNQVFLKIANVDTADTATYYCARLFTTTTSGYFDVWGAGTTVTV
SSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIAA

Sequence of entity 2 (B, E), FASTA

>4YR6_2 light chain of 5G6 (chains B, E)
DIQMTQSPASLSASVGETVTITCRASGNIYNYLAWYQQKQGKSPQLLVYNAKTLADGVPS
RFSGSGSGTQYSLKINSLQPEDFGSYFCQHFWDTPWTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C, F), FASTA

>4YR6_3 ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU (chains C, F)
XKLRGVLQGHL

Primary citation

Structural basis for the specific inhibition of glycoprotein Ib alpha shedding by an inhibitory antibody. Tao, Y., Zhang, X., Liang, X. et al. Sci Rep (2016) 6:24789-24789. DOI 10.1038/srep24789 · PubMed

Other PDB entries of the same protein (UniProt P07359 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CH2 1.6 Å, Low-salt crystal structure of a thrombin-GpIbalpha peptide complex
1P9A 1.7 Å, Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha…
4CH8 1.75 Å, High-salt crystal structure of a thrombin-GpIbalpha peptide complex
1M0Z 1.85 Å, Crystal Structure of the von Willebrand Factor Binding Domain of Glycoprotein Ib alpha
3P72 1.9 Å, structure of platelet Glycoprotein 1b alpha with a bound peptide inhibitor
4C2A 2.08 Å, Crystal Structure of High-Affinity von Willebrand Factor A1 domain with R1306Q and…
8WE2 2.11 Å, 14-3-3 zeta complexed with S609 phosphorylated peptide derived from GPIb alpha…
1OOK 2.3 Å, Crystal Structure of the Complex of Platelet Receptor GPIb-alpha and Human alpha-Thrombin
2BP3 2.32 Å, Crystal structure of Filamin A domain 17 and GPIb alpha cytoplasmic domain complex
8WF6 2.47 Å, 14-3-3 zeta complexed with S559 phosphorylated peptide derived from GPIb alpha…
1P8V 2.6 Å, Crystal structure of the complex of platelet receptor gpib-alpha and alpha-thrombin at…
1SQ0 2.6 Å, Crystal Structure of the Complex of the Wild-type Von Willebrand Factor A1 domain and…

Browse structure collections

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