6O4A: PDB entry 6O4A

Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed with SF355. Determined by X-ray diffraction at 2.1 Å resolution. Released 12 Feb 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Saccharomyces cerevisiae, Burkholderia pseudomallei (strain 1710b)
Chains: 4
Atoms: 6,274
Mol. weight: 93.81 kDa
Ligands: CA, LLD
Released: 12 Feb 2020

Explore 6O4A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O4A contains 25 α-helices and 64 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: 7 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
β-strand	-11--6	6	1
β-strand	4-5	2	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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-75--69	7	5
β-strand	-64--58	7	5
α-helix	-52--43	10
α-helix	-38--36	3
β-strand	-35--31	5	5
β-strand	-28--27	2	5
α-helix	-26--25	2
β-strand	-11--5	7	5
β-strand	3-5	3	6
β-strand	11-16	6	6
β-strand	22	1	7
α-helix	23	1
β-strand	28-37	10	6
β-strand	42-45	4	6
β-strand	53-56	4	6
α-helix	64-69	6
β-strand	74	1	7
β-strand	78-83	6	6
α-helix	85-87	3
β-strand	94	1	4
β-strand	98	1	4
β-strand	104-110	7	6

Chain C: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-75--69	7	8
β-strand	-64--58	7	8
α-helix	-52--43	10
β-strand	-34--31	4	8
β-strand	-28--27	2	8
α-helix	-26--25	2
β-strand	-11--6	6	8
β-strand	4-5	2	9
β-strand	11-16	6	9
α-helix	21	1
β-strand	22	1	10
α-helix	23	1
β-strand	28-37	10	9
β-strand	42-45	4	9
β-strand	53-56	4	9
α-helix	64-69	6
β-strand	74	1	10
β-strand	78-83	6	9
α-helix	85-87	3
β-strand	94	1	11
β-strand	98	1	11
β-strand	104-112	9	9

Chain D: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-75--68	8	12
β-strand	-65--58	8	12
α-helix	-52--43	10
α-helix	-38--36	3
β-strand	-35--31	5	12
β-strand	-28--27	2	12
α-helix	-26--25	2
β-strand	-11--5	7	12
β-strand	4-5	2	13
β-strand	11-16	6	13
β-strand	22	1	14
α-helix	23	1
β-strand	28-37	10	13
β-strand	42-45	4	13
β-strand	53-56	4	13
α-helix	64-69	6
β-strand	74	1	14
β-strand	78-83	6	13
α-helix	85-87	3
β-strand	94	1	11
β-strand	98	1	11
β-strand	104-110	7	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein SMT3,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

>6O4A_1 Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase (chains A, B, C, D)
MGHHHHHHSGEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDS
LRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTVVTTESGLKYEDLTEGSGAEAR
AGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIP
PQLGYGARGAGGVIPPNATLVFEVELLDV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
LLD	2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2…	C21 H25 N3 O5 S	4

Primary citation

CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355. Iwasaki, J., Lorimer, D.D., Vivoli, M. 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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