4J2O: PDB entry 4J2O

Crystal structure of NADP-bound WbjB from A. baumannii community strain D1279779. Determined by X-ray diffraction at 2.65 Å resolution. Released 17 Apr 2013.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Acinetobacter baumannii
Chains: 6
Atoms: 15,097
Mol. weight: 254.26 kDa
Ligands: NAP
Released: 17 Apr 2013

Explore 4J2O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4J2O contains 121 α-helices and 102 β-strands across 6 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: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	6-10	5	2
α-helix	15-24	10
β-strand	29	1	1
β-strand	31-36	6	2
α-helix	39-49	11
β-strand	54-58	5	2
α-helix	64-70	7
β-strand	76-79	4	2
α-helix	86-91	6
α-helix	93-96	4
α-helix	97-102	6
α-helix	103-113	11
β-strand	118-124	7	2
α-helix	125-127	3
α-helix	133-149	17
β-strand	158-164	7	2
α-helix	166-167	2
α-helix	174-183	10
α-helix	186-187	2
β-strand	188-190	3	3
β-strand	196-198	3	4
α-helix	202-215	14
β-strand	221-224	4	2
β-strand	228-230	3	4
α-helix	231-241	11
β-strand	249-251	3	3
α-helix	254-255	2
β-strand	263-265	3	5
α-helix	267-272	6
β-strand	274-275	2	2
β-strand	279-282	4	2
α-helix	283-285	3
β-strand	308-309	2	5
α-helix	314	1
β-strand	315	1	4
α-helix	316	1
α-helix	318-325	8
α-helix	329-332	4

Chain B: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
β-strand	6-10	5	7
α-helix	15-24	10
β-strand	29	1	6
β-strand	31-36	6	7
α-helix	39-49	11
β-strand	54-58	5	7
α-helix	64-70	7
β-strand	76-79	4	7
α-helix	86-91	6
α-helix	93-96	4
α-helix	97-102	6
α-helix	103-113	11
β-strand	118-124	7	7
α-helix	125-127	3
α-helix	133-148	16
β-strand	158-164	7	7
α-helix	166-167	2
α-helix	174-183	10
α-helix	186-187	2
β-strand	188-189	2	8
β-strand	196-198	3	9
α-helix	202-215	14
β-strand	221-224	4	7
β-strand	228-230	3	9
α-helix	231-241	11
β-strand	249-250	2	8
β-strand	263-265	3	10
α-helix	267-272	6
β-strand	274-275	2	7
β-strand	279-282	4	7
β-strand	308-309	2	10
α-helix	314	1
β-strand	315	1	9
α-helix	316	1
α-helix	318-325	8
α-helix	329-334	6

Chain C: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	11
α-helix	15-24	10
β-strand	31-36	6	11
α-helix	39-49	11
β-strand	54-58	5	11
α-helix	64-70	7
β-strand	76-79	4	11
α-helix	86-91	6
α-helix	93-96	4
α-helix	97-102	6
α-helix	103-113	11
β-strand	118-124	7	11
α-helix	125-127	3
α-helix	133-148	16
β-strand	158-164	7	11
α-helix	166-167	2
α-helix	174-183	10
α-helix	186-187	2
β-strand	188-190	3	12
β-strand	196-198	3	13
α-helix	202-215	14
β-strand	221-224	4	11
β-strand	228-230	3	13
α-helix	231-241	11
β-strand	249-251	3	12
α-helix	254-255	2
β-strand	263-265	3	14
α-helix	267-272	6
α-helix	273	1
β-strand	274-275	2	11
β-strand	279-282	4	11
β-strand	308-309	2	14
α-helix	314	1
β-strand	315	1	13
α-helix	316	1
α-helix	318-325	8
α-helix	329-334	6

Chain D: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
β-strand	6-10	5	16
α-helix	15-24	10
β-strand	29	1	15
β-strand	31-36	6	16
α-helix	39-49	11
β-strand	54-58	5	16
α-helix	64-70	7
β-strand	76-79	4	16
α-helix	86-91	6
α-helix	93-96	4
α-helix	97-102	6
α-helix	103-113	11
β-strand	118-124	7	16
α-helix	125-127	3
α-helix	133-148	16
β-strand	158-164	7	16
α-helix	166-167	2
α-helix	174-183	10
α-helix	186-188	3
β-strand	189-190	2	17
β-strand	196-198	3	18
α-helix	202-215	14
β-strand	221-224	4	16
β-strand	228-230	3	18
α-helix	231-242	12
β-strand	250-251	2	17
α-helix	254-255	2
β-strand	263-265	3	19
α-helix	267-272	6
α-helix	273	1
β-strand	274-275	2	16
β-strand	279-282	4	16
β-strand	308-309	2	19
α-helix	314	1
β-strand	315	1	18
α-helix	316	1
α-helix	318-325	8
α-helix	329-335	7

Chain E: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	20
β-strand	6-10	5	21
α-helix	15-24	10
β-strand	29	1	20
β-strand	31-36	6	21
α-helix	39-49	11
β-strand	54-58	5	21
α-helix	64-70	7
β-strand	76-79	4	21
α-helix	86-91	6
α-helix	93-96	4
α-helix	97-102	6
α-helix	103-113	11
β-strand	118-124	7	21
α-helix	125-127	3
α-helix	133-148	16
β-strand	158-164	7	21
α-helix	166-167	2
α-helix	174-183	10
α-helix	186-188	3
β-strand	196-198	3	22
α-helix	202-215	14
β-strand	221-224	4	21
β-strand	228-230	3	22
α-helix	231-241	11
β-strand	263-265	3	23
α-helix	267-272	6
β-strand	274-275	2	21
β-strand	279-282	4	21
β-strand	308-309	2	23
α-helix	314	1
β-strand	315	1	22
α-helix	316	1
α-helix	318-325	8
α-helix	329-332	4

Chain F: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	24
β-strand	6-10	5	25
α-helix	15-24	10
β-strand	29	1	24
β-strand	31-36	6	25
α-helix	39-49	11
β-strand	54-58	5	25
α-helix	64-70	7
β-strand	76-79	4	25
α-helix	86-91	6
α-helix	93-96	4
α-helix	97-102	6
α-helix	103-113	11
β-strand	118-124	7	25
α-helix	125-127	3
α-helix	133-148	16
β-strand	158-164	7	25
α-helix	166-167	2
α-helix	174-183	10
α-helix	186-188	3
β-strand	196-198	3	26
α-helix	202-215	14
β-strand	221-224	4	25
β-strand	228-230	3	26
α-helix	231-241	11
β-strand	263-265	3	27
α-helix	267-272	6
α-helix	273	1
β-strand	274-275	2	25
β-strand	279-282	4	25
β-strand	308-309	2	27
α-helix	314	1
β-strand	315	1	26
α-helix	316	1
α-helix	318-325	8
α-helix	329-332	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase	A, B, C, D, E, F	protein	363	Acinetobacter baumannii	P37362 (AlphaFold model)

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

>4J2O_1 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase (chains A, B, C, D, E, F)
MGSSHHHHHHSSGLVPRGSMFKDKVLLITGGTGSFGNAVLKRFLETDIKEIRIFSRDEKK
QDDMRKKYHSAKLKFYIGDVRDYNSILNATRGVDYIYHAAALKQVPSCEFHPMEAVKTNV
LGTENVLEAAIQNHVKRVVCLSTDKAVYPINAMGISKAMMEKVMVAKSRNLEGLDTVICG
TRYGNVMASRGSVIPLFVDQIRQGKPLTITDPNMTRFMMTLEDAVDLVLYAFEHGENGDI
FVQKAPAATIAVLAEALKQLLNVEDHPISIMGTRHGEKAFEALLSREEMVHAFDQGDYFR
VPADQRDLNYEKYVEDGDLKITEFEDYNSHNTTRLDVEGMKQLLLKLDFVRALTRGEYIS
PEA

Ligands and cofactors

ID	Name	Formula	Copies
NAP	NADP nicotinamide-adenine-dinucleotide phosphate	C21 H28 N7 O17 P3	6

Primary citation

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii. Shah, B.S., Ashwood, H.E., Harrop, S.J. et al. PLoS One (2018) 13:e0191610-e0191610. DOI 10.1371/journal.pone.0191610 · PubMed

Other PDB entries of the same protein (UniProt P37362 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HY9 1.55 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with…
4HYB 1.7 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with…
4EZN 1.8 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with…
4EZQ 2.0 Å, Crystal structure of the substrate binding domain of E.coli DnaK in complex with the…
3DPO 2.1 Å, Crystal structure of the substrate binding domain of E. coli DnaK in complex with a…
3DPP 2.5 Å, Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long…
3DPQ 2.6 Å, Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long…
5HD1 2.7 Å, Crystal structure of antimicrobial peptide Pyrrhocoricin bound to the Thermus…
5FDV 2.8 Å, Crystal structure of the Pyrrhocoricin antimicrobial peptide bound to the Thermus…

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