4GGQ: PDB entry 4GGQ

Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40. Determined by X-ray diffraction at 1.95 Å resolution. Released 15 Aug 2012.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Saccharomyces cerevisiae, Burkholderia pseudomallei
Chains: 4
Atoms: 5,991
Mol. weight: 94.16 kDa
Ligands: 861, CA
Released: 15 Aug 2012

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

Secondary structure: helices and β-sheets

4GGQ contains 33 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.

Chains A and C: 9 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
α-helix	21	1
β-strand	22	1	7
α-helix	23	1
β-strand	28-37	10	6
β-strand	42-45	4	6
α-helix	46-49	4
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	8
β-strand	98	1	8
α-helix	99	1
β-strand	104-112	9	6

Chain B: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-75--69	7	9
β-strand	-64--58	7	9
α-helix	-52--43	10
α-helix	-38--36	3
β-strand	-34--31	4	9
β-strand	-28--27	2	9
α-helix	-26--25	2
β-strand	-11--6	6	9
β-strand	3-5	3	10
β-strand	11-16	6	10
α-helix	21	1
β-strand	22	1	11
α-helix	23	1
β-strand	28-37	10	10
β-strand	42-45	4	10
α-helix	46-49	4
β-strand	53-56	4	10
α-helix	64-69	6
β-strand	74	1	11
β-strand	78-83	6	10
α-helix	85-87	3
β-strand	94	1	12
β-strand	98	1	12
β-strand	104-112	9	10

Chain D: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-75--69	7	13
β-strand	-63--58	6	13
α-helix	-52--43	10
β-strand	-33--31	3	13
β-strand	-28--27	2	13
α-helix	-26--25	2
β-strand	-11--7	5	13
β-strand	3-5	3	14
β-strand	11-16	6	14
α-helix	21	1
β-strand	22	1	15
α-helix	23	1
β-strand	28-37	10	14
β-strand	42-45	4	14
α-helix	46-49	4
β-strand	53-56	4	14
α-helix	64-69	6
β-strand	74	1	15
β-strand	78-83	6	14
α-helix	85-87	3
β-strand	94	1	16
β-strand	98	1	16
β-strand	104-112	9	14

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	Q12306 (AlphaFold model), Q3JK38 (AlphaFold model)

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

>4GGQ_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
861	3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate	C25 H33 N O7 S	4
CA	Calcium ion	Ca	2

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

Primary citation

A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. Begley, D.W., Fox, D., Jenner, D. et al. Antimicrob Agents Chemother (2014) 58:1458-1467. DOI 10.1128/AAC.01875-13 · PubMed

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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