4KHZ: Maltose-binding periplasmic protein

Crystal structure of the maltose-binding protein/maltose transporter complex in an pre-translocation conformation bound to maltoheptaose. Determined by X-ray diffraction at 2.9 Å resolution. Released 23 Oct 2013.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Escherichia coli
Chains: 5
Atoms: 14,715
Mol. weight: 217.49 kDa
Ligands: PGV
Released: 23 Oct 2013

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

Secondary structure: helices and β-sheets

4KHZ contains 96 α-helices and 102 β-strands across 5 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: 14 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	20
β-strand	16-25	10	20
β-strand	31-35	5	21
α-helix	42-50	9
β-strand	57-62	6	20
β-strand	66	1	20
α-helix	72-75	4
β-strand	77-80	4	21
α-helix	92-101	10
α-helix	107-121	15
α-helix	124-126	3
α-helix	136-150	15
β-strand	154-158	5	21
α-helix	166-183	18
β-strand	187-191	5	21
α-helix	194-200	7
β-strand	203-208	6	21
β-strand	211-216	6	21
α-helix	218-223	6
β-strand	227	1	22
α-helix	228-233	6
α-helix	238-239	2
β-strand	240-249	10	23
β-strand	254-257	4	23
β-strand	265-268	4	23
β-strand	270	1	24
β-strand	280-285	6	23
β-strand	291-292	2	25
β-strand	299-309	11	25
β-strand	313-319	7	25
α-helix	326	1
β-strand	327-332	6	25
β-strand	342-346	5	25
α-helix	349-351	3
β-strand	353-355	3	23
β-strand	360	1	22
β-strand	361	1	23
α-helix	362	1
β-strand	364	1	24

Chain B: 13 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	26
β-strand	17-25	9	26
β-strand	31-35	5	27
α-helix	42-50	9
β-strand	57-61	5	26
β-strand	66	1	26
α-helix	72-74	3
β-strand	77-80	4	27
α-helix	92-96	5
α-helix	98-101	4
α-helix	107-121	15
α-helix	136-150	15
β-strand	154-158	5	27
α-helix	166-183	18
β-strand	186-191	6	27
α-helix	194-200	7
β-strand	203-207	5	27
β-strand	212-216	5	27
α-helix	218-223	6
β-strand	227	1	28
α-helix	228-233	6
α-helix	238-239	2
β-strand	240-249	10	29
β-strand	254-257	4	29
β-strand	265-268	4	29
β-strand	270	1	30
β-strand	280-285	6	29
β-strand	291-292	2	31
β-strand	299-309	11	31
β-strand	313-319	7	31
β-strand	327-332	6	31
β-strand	342-346	5	31
α-helix	349-351	3
β-strand	353-355	3	29
β-strand	360	1	28
β-strand	361-362	2	29
α-helix	363	1
β-strand	364	1	30

Chain E: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	7-10	4	1
α-helix	17-31	15
β-strand	35-38	4	1
α-helix	43-52	10
β-strand	59-63	5	1
α-helix	64-66	3
α-helix	67-73	7
β-strand	76-77	2	1
α-helix	78-79	2
α-helix	83-86	4
β-strand	89	1	2
α-helix	91-96	6
β-strand	98	1	3
β-strand	103	1	3
β-strand	106-111	6	1
β-strand	114-118	5	4
β-strand	128	1	5
α-helix	132-142	11
β-strand	145-147	3	4
α-helix	154-163	10
β-strand	167-172	6	6
β-strand	175-182	8	6
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	4
α-helix	229-231	3
α-helix	232-238	7
β-strand	242-245	4	4
α-helix	246-248	3
β-strand	249	1	5
α-helix	254-255	2
β-strand	258-259	2	7
β-strand	260-267	8	1
α-helix	273-278	6
α-helix	279-284	6
α-helix	287-296	10
β-strand	301-302	2	1
β-strand	304	1	2
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	7
α-helix	330-331	2
α-helix	335-352	18
α-helix	357-369	13

Chain F: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	20-35	16
α-helix	44-58	15
α-helix	65-75	11
α-helix	76-80	5
α-helix	81-88	8
α-helix	89-91	3
β-strand	92	1	8
β-strand	95	1	9
β-strand	100	1	10
α-helix	102-111	10
β-strand	113-121	9	11
β-strand	123-127	5	12
β-strand	130-136	7	12
β-strand	143-145	3	12
β-strand	149	1	12
β-strand	155	1	13
β-strand	158	1	14
β-strand	160-162	3	12
α-helix	165-166	2
α-helix	169-172	4
α-helix	173-178	6
α-helix	180-185	6
β-strand	186	1	13
β-strand	188-189	2	14
β-strand	195-196	2	14
β-strand	197-198	2	11
β-strand	203-209	7	11
β-strand	211-213	3	15
β-strand	219-221	3	15
β-strand	227-228	2	15
β-strand	229-231	3	16
β-strand	236-238	3	16
β-strand	250-251	2	16
β-strand	255	1	10
β-strand	258	1	8
α-helix	263-269	7
α-helix	271-306	36
α-helix	314-326	13
α-helix	329-339	11
α-helix	346-351	6
α-helix	365-392	28
α-helix	398-406	9
α-helix	410-413	4
α-helix	414-418	5
α-helix	419-438	20
α-helix	441-447	7
β-strand	453	1	17
α-helix	454	1
β-strand	462	1	17
α-helix	467-475	9
β-strand	483	1	9
α-helix	484-504	21

Chain G: 20 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	10-38	29
α-helix	57-63	7
β-strand	67-68	2	18
β-strand	74-75	2	18
α-helix	81-111	31
α-helix	118-129	12
α-helix	133-135	3
α-helix	138-150	13
α-helix	152-154	3
α-helix	159-166	8
α-helix	171-181	11
α-helix	186-194	9
α-helix	199-202	4
α-helix	203-207	5
α-helix	208-210	3
α-helix	212-228	17
α-helix	231-236	6
α-helix	240-242	3
α-helix	245-248	4
β-strand	253-254	2	19
β-strand	257-258	2	19
α-helix	260-270	11
α-helix	272-280	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein	E	protein	380	Escherichia coli	P0AEX9 (AlphaFold model)
Maltose transport system permease protein MalF	F	protein	514	Escherichia coli	P02916 (AlphaFold model)
Binding-protein-dependent transport systems inner membrane component	G	protein	296	Escherichia coli	P68183 (AlphaFold model)
Binding-protein-dependent transport systems inner membrane component	A, B	protein	381	Escherichia coli	P68187 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>4KHZ_1 Maltose-binding periplasmic protein (chains E)
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEA
LKDAQTRITKASASHHHHHH

Sequence of entity 2 (F), FASTA

>4KHZ_2 Maltose transport system permease protein MalF (chains F)
MDVIKKKHWWQSDALKWSVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLYIFANR
KAYAWRYVYPGMAGMGLFVLFPLVCTIAIAFTNYSSTNQLTFERAQEVLLDRSWQAGKTY
NFGLYPAGDEWQLALSDGETGKNYLSDAFKFGGEQKLQLKETTAQPEGERANLRVITQNR
QALSDITAILPDGNKVMMSSLRQFSGTQPLYTLDGDGTLTNNQSGVKYRPNNQIGFYQSI
TADGNWGDEKLSPGYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGM
VLACLVQWEALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGVKPA
WFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLP
LLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGG
GQDFGLAAAIATLIFLLVGALAIVNLKATRMKFD

Sequence of entity 3 (G), FASTA

>4KHZ_3 Binding-protein-dependent transport systems inner membrane component (chains G)
MAMVQPKSQKARLFITHLLLLLFIAAIMFPLLMVVAISLRQGNFATGSLIPEQISWDHWK
LALGFSVEQADGRITPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKAT
LLKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGY
FETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDV
NSYTLAVGMQQYLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG

Sequence of entity 4 (A, B), FASTA

>4KHZ_4 Binding-protein-dependent transport systems inner membrane component (chains A, B)
MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL
FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEV
LQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLH
KRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMN
FLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVIL
EGEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGT
ACRRLHKEPGVASASHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PGV	(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo…	C40 H77 O10 P	1

Primary citation

Structural basis for substrate specificity in the Escherichia coli maltose transport system. Oldham, M.L., Chen, S., Chen, J. Proc Natl Acad Sci U S A (2013) 110:18132-18137. DOI 10.1073/pnas.1311407110 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

Browse structure collections

About this viewer

MolViewer shows 4KHZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.