5KLX: PDB entry 5KLX

Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110. Determined by X-ray diffraction at 2.45 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Saccharomyces cerevisiae, Burkholderia pseudomallei (strain 1710b)
Chains: 4
Atoms: 5,458
Mol. weight: 94.03 kDa
Ligands: 6UO, MG
Released: 31 May 2017

Explore 5KLX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KLX contains 34 α-helices and 67 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: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-75--69	7	1
β-strand	-64--58	7	1
α-helix	-52--43	10
α-helix	-38--36	3
β-strand	-34--31	4	1
β-strand	-28--27	2	1
α-helix	-26--25	2
α-helix	-19--17	3
α-helix	-15--14	2
β-strand	-10--6	5	1
β-strand	3-5	3	2
β-strand	11-16	6	2
α-helix	21	1
β-strand	22	1	3
α-helix	23	1
β-strand	28-37	10	2
β-strand	42-45	4	2
β-strand	53-56	4	2
α-helix	64-69	6
β-strand	74	1	3
β-strand	78-83	6	2
α-helix	85-87	3
β-strand	94	1	4
β-strand	98	1	4
β-strand	104-112	9	2

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	-75--74	2	5
β-strand	-71--69	3	6
β-strand	-64--62	3	6
β-strand	-59--58	2	5
α-helix	-53--43	11
α-helix	-38--36	3
β-strand	-33--31	3	7
β-strand	-28--27	2	7
α-helix	-26--25	2
α-helix	-20--17	4
β-strand	-10--9	2	6
β-strand	-8--7	2	7
β-strand	4-5	2	8
β-strand	11-16	6	8
β-strand	22	1	9
β-strand	28-37	10	8
β-strand	42-45	4	8
α-helix	46-48	3
β-strand	53-56	4	8
α-helix	64-69	6
β-strand	74	1	9
β-strand	78-83	6	8
α-helix	85-87	3
β-strand	94	1	10
β-strand	98	1	10
β-strand	104-112	9	8

Chain C: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-74--69	6	11
β-strand	-64--59	6	11
α-helix	-52--44	9
α-helix	-38--36	3
β-strand	-33--31	3	11
β-strand	-28--27	2	11
α-helix	-20--17	4
α-helix	-15--14	2
β-strand	-11--7	5	11
β-strand	3-5	3	12
β-strand	11-16	6	12
α-helix	21	1
β-strand	22	1	13
α-helix	23	1
β-strand	28-37	10	12
β-strand	42-45	4	12
α-helix	47-49	3
β-strand	53-56	4	12
α-helix	64-69	6
α-helix	73	1
β-strand	74	1	13
β-strand	78-83	6	12
α-helix	85-87	3
β-strand	94	1	14
β-strand	98	1	14
α-helix	102-103	2
β-strand	104-112	9	12

Chain D: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-75--69	7	15
β-strand	-64--58	7	15
α-helix	-52--43	10
β-strand	-33--31	3	15
β-strand	-28--27	2	15
α-helix	-26--25	2
β-strand	-11--7	5	15
β-strand	3-5	3	16
β-strand	11-16	6	16
α-helix	21	1
β-strand	22	1	17
α-helix	23	1
β-strand	28-37	10	16
β-strand	42-45	4	16
β-strand	53-56	4	16
α-helix	64-69	6
β-strand	74	1	17
β-strand	78-83	6	16
α-helix	85-87	3
β-strand	94	1	18
β-strand	98	1	18
α-helix	99	1
β-strand	104-112	9	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase	A, B, C, D	protein	209	Saccharomyces cerevisiae, Burkholderia pseudomallei (strain 1710b)	Q12306 (AlphaFold model), Q3JK38 (AlphaFold model)

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

>5KLX_1 Chimera protein of Ubiquitin-like protein SMT3 and Peptidyl-prolyl cis-trans isomerase (chains A, B, C, D)
MGHHHHHHSGEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDS
LRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTVVTTESGLKYEDLTEGSGAEAR
AGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIP
PQLGYGARGAGGVIPPNATLVFEVELLDV

Ligands and cofactors

ID	Name	Formula	Copies
6UO	2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl…	C21 H24 N2 O6 S	4
MG	Magnesium ion	Mg	2

Water and common crystallization additives (IMD, PEG) are not listed.

Primary citation

Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110. Lorimer, D.D., Fox III, D., Seufert, F. et al. To be published.

Other PDB entries of the same protein (UniProt Q12306 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UF8 1.5 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with a G95A…
6UKZ 1.52 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 6
3UQA 1.55 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface…
3VAW 1.55 Å, Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface…
5YCA 1.57 Å, Crystal structure of inner membrane protein Bqt4 in complex with LEM2
7P7W 1.57 Å, N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with…
1EUV 1.6 Å, X-ray structure of the C-terminal ULP1 protease domain in complex with SMT3, the yeast…
6UKU 1.68 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 3
7P7I 1.7 Å, Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides
6UKM 1.74 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound MSA-2
4G50 1.75 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface…
7P9L 1.75 Å, N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with…

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