8R2P: PDB entry 8R2P

YZwIdeal x16 a scaffold for cryo-EM of small proteins of interest crystallizing in space group 19 (P 21 21 21). Determined by X-ray diffraction at 2.22 Å resolution. Released 13 Nov 2024.

Method: X-ray diffraction
Resolution: 2.22 Å
Organism: Escherichia coli
Chains: 4
Atoms: 16,262
Mol. weight: 229.21 kDa
Ligands: PLP
Released: 13 Nov 2024

Explore 8R2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R2P contains 104 α-helices and 76 β-strands across 4 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: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
β-strand	66	1	1
β-strand	67-70	4	2
β-strand	75-78	4	2
β-strand	83-86	4	2
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	3
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	4
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	4
α-helix	185-188	4
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	4
α-helix	215-227	13
β-strand	232-237	6	4
β-strand	241	1	5
β-strand	247	1	5
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	4
α-helix	285-287	3
β-strand	295-298	4	4
α-helix	300-303	4
β-strand	310-315	6	4
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	6
β-strand	390-395	6	6
α-helix	398-410	13
β-strand	413-414	2	2
β-strand	416-417	2	6
β-strand	424-427	4	6
α-helix	435-459	25

Chain B: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
β-strand	66	1	3
β-strand	67-70	4	7
β-strand	75-78	4	7
β-strand	83-86	4	7
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	1
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	8
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	8
α-helix	185-188	4
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	8
α-helix	215-227	13
β-strand	232-237	6	8
β-strand	241	1	9
β-strand	247	1	9
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	8
α-helix	285-287	3
β-strand	295-298	4	8
α-helix	300-303	4
β-strand	310-315	6	8
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	10
β-strand	390-395	6	10
α-helix	398-410	13
β-strand	413-414	2	7
β-strand	416-417	2	10
β-strand	424-427	4	10
α-helix	435-469	35

Chain C: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
β-strand	66	1	11
β-strand	67-70	4	12
β-strand	75-78	4	12
β-strand	83-86	4	12
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	13
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	14
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	14
α-helix	185-188	4
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	14
α-helix	215-227	13
β-strand	232-237	6	14
β-strand	241	1	15
β-strand	247	1	15
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	14
α-helix	285-287	3
β-strand	295-298	4	14
α-helix	300-303	4
β-strand	310-315	6	14
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	16
β-strand	390-395	6	16
α-helix	398-410	13
β-strand	413-414	2	12
β-strand	416-417	2	16
β-strand	424-427	4	16
α-helix	435-464	30

Chain D: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
β-strand	66	1	13
β-strand	67-70	4	17
β-strand	75-78	4	17
β-strand	83-86	4	17
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	11
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	18
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	18
α-helix	185-188	4
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	18
α-helix	215-227	13
β-strand	232-237	6	18
β-strand	241	1	19
β-strand	247	1	19
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	18
α-helix	285-287	3
β-strand	295-298	4	18
α-helix	300-303	4
β-strand	310-315	6	18
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	20
β-strand	390-395	6	20
α-helix	398-410	13
β-strand	413-414	2	17
β-strand	416-417	2	20
β-strand	424-427	4	20
α-helix	435-457	23
α-helix	464-476	13
α-helix	482-494	13
α-helix	496-498	3
α-helix	499-511	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putrescine aminotransferase,Immunoglobulin G-binding protein A	A, B, C, D	protein	523	Escherichia coli	P02976 (AlphaFold model), P42588 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8R2P_1 Putrescine aminotransferase,Immunoglobulin G-binding protein A (chains A, B, C, D)
GSSHHHHHHYYLESASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEY
RKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAK
QPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTF
IATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVA
AVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQP
DILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQ
NLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRV
LVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEALEVSAKEQQNAFYE
ILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPK

Ligands and cofactors

ID	Name	Formula	Copies
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	4

Primary citation

Engineered imaging scaffolds for cryo-EM of small proteins of interest. Moche, M., Nygren, P.A., Nilvebrant, J. To be published.

Other PDB entries of the same protein (UniProt P02976 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8DA5 1.0 Å, Coevolved affibody-Z domain pair LL1.c4
8DA7 1.02 Å, Coevolved affibody-Z domain pair LL1.c6
8DA3 1.06 Å, Coevolved affibody-Z domain pair LL1.c1
8DAB 1.13 Å, Coevolved affibody-Z domain pair LL2.c17
8DAC 1.19 Å, Coevolved affibody-Z domain pair LL2.c22
8DA8 1.29 Å, Coevolved affibody-Z domain pair LL2.c1
8DA9 1.35 Å, Coevolved affibody-Z domain pair LL2.c3
9M6O 1.49 Å, Crystal structure of S. aureus protein A bound to a camelid single-domain antibody
8DA6 1.5 Å, Coevolved affibody-Z domain pair LL1.c5
6K65 1.65 Å, Application of anti-helix antibodies in protein structure determination (9014-1P4B)
5U6A 1.74 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-PEG3-meditope
8DAA 1.75 Å, Coevolved affibody-Z domain pair LL2.c7

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