2RBT: N-methylbenzylamine

n-methylbenzylamine in complex with Cytochrome C Peroxidase W191G. Determined by X-ray diffraction at 1.24 Å resolution. Released 1 Apr 2008.

Method: X-ray diffraction
Resolution: 1.24 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 3,112
Mol. weight: 34.27 kDa
Ligands: PO4, 271, HEM
Released: 1 Apr 2008

Explore 2RBT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2RBT contains 24 α-helices and 11 β-strands across 1 chain. 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 X: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
α-helix	10-11	2
α-helix	16-32	17
α-helix	36-39	4
α-helix	43-54	12
β-strand	58	1	2
β-strand	63	1	2
α-helix	70-72	3
α-helix	74-77	4
α-helix	80-82	3
α-helix	86-98	13
α-helix	104-118	15
β-strand	126	1	3
α-helix	135-137	3
α-helix	138-140	3
α-helix	145-146	2
α-helix	151-159	9
α-helix	165-172	8
α-helix	173-176	4
β-strand	179-180	2	4
α-helix	182-185	4
β-strand	189-190	2	4
α-helix	201-208	8
β-strand	212-215	4	5
β-strand	221-224	4	5
β-strand	230-231	2	5
α-helix	233-240	8
α-helix	242-252	11
α-helix	255-271	17
β-strand	274-275	2	1
α-helix	276-277	2
α-helix	281-283	3
β-strand	284	1	3
α-helix	286-288	3
α-helix	289-292	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytochrome C Peroxidase	X	protein	292	Saccharomyces cerevisiae	P00431 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>2RBT_1 Cytochrome C Peroxidase (chains X)
TLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDN
TGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGP
KIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHL
KNSGYEGPGGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDP
KYLSIVKEYANDQDKFFKDFSKAFEKLLEDGITFPKDAPSPFIFKTLEEQGL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
271	N-methyl-1-phenylmethanamine	C8 H11 N	1
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1

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

Primary citation

Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Graves, A.P., Shivakumar, D.M., Boyce, S.E. et al. J Mol Biol (2008) 377:914-934. DOI 10.1016/j.jmb.2008.01.049 · PubMed

Other PDB entries of the same protein (UniProt P00431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3E2O 1.06 Å, Crystal structure of cytochrome c peroxidase, N184R mutant
7BIU 1.06 Å, XFEL crystal structure of cytochrome c peroxidase compound II
2EUT 1.12 Å, Cytochrome c peroxidase (CCP) in complex with 2-amino-4-picoline
1Z53 1.13 Å, The 1.13 Angstrom Structure of Iron-free Cytochrome c Peroxidase
1ZBY 1.2 Å, High-Resolution Crystal Structure of Native (Resting) Cytochrome c Peroxidase (CcP)
2Y5A 1.25 Å, Cytochrome c peroxidase (CCP) W191G bound to 3-aminopyridine
1ZBZ 1.29 Å, High-Resolution Crystal Structure of Compound I intermediate of Cytochrome c Peroxidase…
2AS4 1.3 Å, cytochrome c peroxidase in complex with 3-fluorocatechol
2EUQ 1.3 Å, Cytochrome c peroxydase (CCP) in complex with 3-thienylmethylamine
3E2N 1.3 Å, Engineering ascorbate peroxidase activity into cytochrome c peroxidase
2AQD 1.35 Å, cytochrome c peroxidase (CCP) in complex with 2,5-diaminopyridine
2EUR 1.39 Å, Cytochrome c peroxidase (CCP) in complex with 4-pyridylcarbinol

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