1XXH: ATPgS Bound E. Coli Clamp Loader Complex

ATPgS Bound E. Coli Clamp Loader Complex. Determined by X-ray diffraction at 3.45 Å resolution. Released 7 Dec 2004.

Method: X-ray diffraction
Resolution: 3.45 Å
Organism: Escherichia coli
Chains: 10
Atoms: 27,736
Mol. weight: 404.36 kDa
Ligands: PO4, AGS, ZN
Released: 7 Dec 2004

Explore 1XXH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1XXH contains 198 α-helices and 78 β-strands across 10 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: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6-15	10
β-strand	20-25	6	1
α-helix	28-42	15
β-strand	51-54	4	1
α-helix	61-69	9
α-helix	70-72	3
β-strand	79-83	5	1
α-helix	93-99	7
β-strand	109-114	6	1
α-helix	121-123	3
α-helix	126-130	5
β-strand	135-139	5	1
α-helix	147-157	11
β-strand	161-162	2	2
α-helix	164-172	9
α-helix	178-191	14
β-strand	196-197	2	2
α-helix	199-209	11
α-helix	214-221	8
α-helix	226-235	10
α-helix	243-262	20
α-helix	269-276	8
α-helix	285-292	8
α-helix	295-314	20
α-helix	321-330	10

Chain B: 23 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-33	12
β-strand	41-44	4	3
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-94	5	3
α-helix	103-109	7
β-strand	122-126	5	3
α-helix	128-130	3
α-helix	133-144	12
β-strand	152-156	5	3
α-helix	164-168	5
β-strand	171-174	4	3
α-helix	175-176	2
α-helix	180-192	13
β-strand	198	1	4
α-helix	200-209	10
α-helix	214-228	15
β-strand	232	1	4
α-helix	234-240	7
α-helix	248-254	7
α-helix	255-259	5
α-helix	261-274	14
α-helix	279-295	17
α-helix	304-306	3
α-helix	310-319	10
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14

Chain C: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	23-34	12
β-strand	40-44	5	5
β-strand	47	1	6
β-strand	49	1	6
α-helix	51-59	9
α-helix	77-82	6
β-strand	87	1	5
β-strand	90-94	5	5
α-helix	101-109	9
β-strand	121-126	6	5
α-helix	133-144	12
β-strand	150-156	7	5
α-helix	164-167	4
β-strand	171	1	5
β-strand	174	1	5
α-helix	176-179	4
α-helix	180-192	13
β-strand	197-198	2	7
α-helix	200-209	10
α-helix	214-227	14
β-strand	231-232	2	7
α-helix	234-241	8
α-helix	246-257	12
α-helix	263-273	11
α-helix	278-295	18
α-helix	307-319	13
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
α-helix	364-366	3

Chain D: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-32	11
β-strand	40-45	6	8
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-94	5	8
α-helix	101-109	9
β-strand	121-126	6	8
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	8
α-helix	159-161	3
α-helix	164-169	6
β-strand	171-175	5	8
α-helix	176-179	4
α-helix	180-193	14
β-strand	197-198	2	9
α-helix	200-209	10
α-helix	214-227	14
β-strand	231-232	2	9
α-helix	234-241	8
α-helix	248-258	11
α-helix	262-272	11
α-helix	279-297	19
α-helix	305-308	4
α-helix	310-319	10
α-helix	322-338	17
α-helix	345-358	14

Chain E: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	26-30	5	10
α-helix	37-48	12
α-helix	63-70	8
β-strand	76-78	3	10
β-strand	88	1	11
α-helix	90-101	12
α-helix	103-104	2
β-strand	110-113	4	10
α-helix	117-119	3
β-strand	120	1	11
α-helix	122-133	12
β-strand	139-145	7	10
α-helix	153-156	4
β-strand	160-163	4	10
α-helix	165-168	4
α-helix	169-179	11
α-helix	184-192	9
α-helix	198-205	8
α-helix	209-226	18
α-helix	230-232	3
α-helix	233-236	4
α-helix	241-259	19
α-helix	271-280	10
α-helix	283-302	20
α-helix	309-323	15

Chain F: 17 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	12
α-helix	9-15	7
β-strand	20-25	6	12
α-helix	28-42	15
β-strand	51-52	2	12
α-helix	61-70	10
β-strand	79-83	5	12
α-helix	93-96	4
α-helix	98-101	4
β-strand	109-114	6	12
α-helix	125-130	6
β-strand	135-139	5	12
α-helix	147-156	10
β-strand	161-162	2	13
α-helix	164-172	9
α-helix	178-191	14
β-strand	196-197	2	13
α-helix	199-208	10
α-helix	216-220	5
α-helix	226-235	10
α-helix	243-261	19
α-helix	269-275	7
α-helix	282-292	11
α-helix	295-314	20
α-helix	320-330	11

Chain G: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-32	11
β-strand	40-44	5	14
α-helix	51-62	12
α-helix	77-84	8
β-strand	90-94	5	14
α-helix	103-107	5
β-strand	121-126	6	14
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	14
α-helix	159-161	3
α-helix	164-167	4
β-strand	171-174	4	14
α-helix	180-190	11
β-strand	198	1	15
α-helix	204-207	4
α-helix	214-227	14
β-strand	232	1	15
α-helix	234-237	4
α-helix	248-257	10
α-helix	261-272	12
α-helix	278-295	18
α-helix	310-319	10
α-helix	322-338	17
α-helix	345-359	15

Chain H: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	23-34	12
β-strand	40-44	5	16
β-strand	47	1	17
β-strand	49	1	17
α-helix	51-59	9
α-helix	77-82	6
β-strand	91-94	4	16
α-helix	101-109	9
β-strand	121-126	6	16
α-helix	128-130	3
α-helix	133-140	8
β-strand	150-156	7	16
α-helix	164-167	4
β-strand	173-174	2	16
α-helix	176-179	4
α-helix	180-193	14
β-strand	198	1	18
α-helix	203-209	7
α-helix	214-227	14
β-strand	232	1	18
α-helix	234-240	7
α-helix	246-257	12
α-helix	261-272	12
α-helix	278-294	17
α-helix	307-319	13
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III, delta subunit	A, F	protein	343	Escherichia coli	P28630 (AlphaFold model)
DNA polymerase III subunit gamma	B, C, D, G, H, I	protein	373	Escherichia coli	P06710 (AlphaFold model)
DNA polymerase III, delta prime subunit	E, J	protein	334	Escherichia coli	P28631 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>1XXH_1 DNA polymerase III, delta subunit (chains A, F)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

Sequence of entity 2 (B, C, D, G, H, I), FASTA

>1XXH_2 DNA polymerase III subunit gamma (chains B, C, D, G, H, I)
MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAK
GLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRF
KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDV
EQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAM
LGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPA
ALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFH
PRMPLPEPEVPRQ

Sequence of entity 3 (E, J), FASTA

>1XXH_3 DNA polymerase III, delta prime subunit (chains E, J)
MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCG
HCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL
TDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV
TMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQ
APARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQL
MSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	4
ZN	Zinc ion	Zn	8

Primary citation

Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Kazmirski, S.L., Podobnik, M., Weitze, T.F. et al. Proc Natl Acad Sci U S A (2004) 101:16750-16755. DOI 10.1073/pnas.0407904101 · PubMed

Other PDB entries of the same protein (UniProt P28630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1JQL 2.5 Å, Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader…
9OYJ 2.53 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYH 2.54 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYI 2.54 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
8GJ2 2.6 Å, E. coli clamp loader with closed clamp on primed template DNA
9OYK 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYM 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
1JR3 2.7 Å, Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA…
8GIZ 2.7 Å, E. coli clamp loader with open clamp
9OYN 2.7 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYC 2.71 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…
9OYE 2.72 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…

Browse structure collections

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