ArchDB - Biological DataBase of Protein Loops

Information on SUBCLASS 3.1.1

Subclass Accession number: 114
Subclass: 3.1.1
Type: HE alpha-beta
DB: ArchDB-KI

Number of loops: 30

Average sequence ID (%) : 19.6 +/- 5.7
Average RMSD (Å) : 0.81 +/- 0.42

Consensus geometry

d (Å): 9

delta (°): 90-135

theta (°): 135-180

rho (°): 0-45

Consensus Sequence:	XXXhphh
(φψ)-conformation:	aalpabb

Pattern:	x	x	{AILV}	x	x	{AGLMV}	x	{EKL}	x	x	{AGILMPV}	{DHKNR}	{ACFILMVY}	{AFILMV}	{AFILMV}
Conservation:	-0.798	0.178	1.936	-0.539	-0.840	-0.723	-0.872	1.395	-0.783	-0.403	-0.650	0.589	-0.815	1.636	0.690

Loops included in this Subclass

Loop	PDB	Chain	Start	End	Sequence	Sec Struct	Ramachandran
16pk_*_224	16pk	-	224	238	IQLLDNMLQRIDYLL	HHHHHHHGGG-SEEE	aaaaaaaaaababbb
1a3w_A_193	1a3w	A	197	211	EDLRFGVKNGVHMVF	HHHHHHHHHT-SEEE	aaaaaaaaavxabbx
1a3w_A_312	1a3w	A	316	329	SDVGNAILDGADCV.	HHHHHHHHHT-SEE.	aaaaaaaaagpabb.
1a3w_A_34	1a3w	A	35	49	ETLVALRKAGLNIVR	HHHHHHHHHT--SEE	aaaaaaaaaNxaxbx
1a3w_A_378	1a3w	A	385	399	SAVAAVFEQKAKAII	HHHHHHHHHT-S-EE	aaaaaaaaavxaebx
1a3x_A_312	1a3x	A	316	329	SDVGNAILDGADCV.	HHHHHHHHTT-SEE.	aNaaaaaaagxabb.
1a49_A_222	1a49	A	226	240	QDLKFGVEQDVDMVF	HHHHHHHHTT-SEEE	aaaaaaaaalxabbx
1a49_A_341	1a49	A	345	359	SDVANAVLDGADCIM	HHHHHHHHHT-SEEE	aaaaaaaaagxabbb
1a49_A_407	1a49	A	414	428	GSVEASYKCLAAALI	HHHHHHHHHT-SEEE	aaaaaaaaavpabbb
1a49_A_57	1a49	A	58	72	ETLKEMIKSGMNVAR	HHHHHHHHTT--EEE	aaaaaaaaagpabbb
1aqf_A_222	1aqf	A	226	240	QDLKFGVEQDVDMVF	HHHHHHHHHT-SEEE	aaaaaaaaavxabbb
1aqf_A_341	1aqf	A	345	359	SDVANAVLDGADCIM	HHHHHHHHHT-SEEE	aaaaaaaaagbabbb
1aqf_A_407	1aqf	A	414	428	GSVEASYKCLAAALI	HHHHHHHHHT-SEEE	aaaaaaaaavpabxb
1aqf_A_57	1aqf	A	58	72	ETLKEMIKSGMNVAR	HHHHHHHHHT--EEE	aaaaaaaaaNpabxb
1pkm_*_222	1pkm	-	226	240	QDLKFGVEQDVDMVF	HHHHHHHHTT-SEEE	aaaaaaaaalxabbx
1pkm_*_341	1pkm	-	345	359	SDVANAVLDGADCIM	HHHHHHHHHT-SEEE	aaaaaaaaagpabbb
1pkm_*_407	1pkm	-	414	428	GSVEASYKCLAAALI	HHHHHHHHHT-S-EE	aaaaaaaaalxabbb
1pkn_*_222	1pkn	-	226	240	QDLKFGVDEDVDMVF	HHHHHHHHHT-SEEE	aaaaaaaaavxabbx
1pkn_*_341	1pkn	-	345	359	SDVANAVLDGADCIM	HHHHHHHHTT-SEEE	aaaaaaaaavxabbb
1pkn_*_407	1pkn	-	414	428	GSVEASYKCLAAALI	HHHHHHHHTT-S-EE	aaaaaaaaalpabbb
1pkn_*_57	1pkn	-	58	72	ETLKEMIKSGMNVAR	HHHHHHHHHT--EEE	aaaaaaaaaNpabbx
1pky_A_172	1pky	A	176	190	QDLIFGCEQGVDFVA	HHHHHHHHHT-SEEE	aaaaaaaaavxabbx
1pky_A_292	1pky	A	296	310	GDVANAILDGTDAVM	HHHHHHHHHT-SEEE	aaaaaaaaagpabbb
1pky_A_354	1pky	A	361	375	GAVETAEKLDAPLIV	HHHHHHHHHT-SEEE	aaaaaaaaalxabbx
1pky_A_382	1pky	A	382	396	KSARAVRKYFPDATI	HHHHHHHTT--SSEE	aaaaaaaaalpaxxx
1qpg_*_37	1qpg	-	44	58	PTIKYVLEHHPRYVV	HHHHHHHTT--SEEE	aaaaaaaaalxabbb
1uky_*_78	1uky	-	87	101	NAISDNVKANKHKFL	HHHHHHHHTT--EEE	aaaaaaaaavbabbb
1ukz_*_78	1ukz	-	87	101	NAISDNVKANKHKFL	HHHHHHHHTT--EEE	aaaaaaaaavbabbb
3bif_A_96	3bif	A	112	126	DVRKFLSEEGGHVAV	HHHHHHHTS--SEEE	aaaaaaaaavxabbb
4tmk_*_16	4tmk	-	22	36	VVVETLEQLGIRDMV	HHHHHHHHTT---EE	aaaaaaaaavbaxbb

PDB ligands within a cut-off distance of 6 Å in this subclass

Loop	PDB	Chain	Ligands	Residue
1a3w_A_34	1a3w	A	PGA2-PHOSPHOGLYCOLIC ACID	R - 49
1a3w_A_378	1a3w	A	FBPFRUCTOSE-1,6-DIPHOSPHATE	T - 379
1a3w_A_378	1a3w	A	FBPFRUCTOSE-1,6-DIPHOSPHATE	L - 401
1a49_A_57	1a49	A	OXLOXALATE ION	R - 72
1a49_A_57	1a49	A	MGMAGNESIUM ION	R - 72
1a49_A_57	1a49	A	ATPADENOSINE-5'-TRIPHOSPHATE	R - 72
1a49_A_57	1a49	A	MGMAGNESIUM ION	N - 74
1a49_A_57	1a49	A	ATPADENOSINE-5'-TRIPHOSPHATE	N - 74
1a49_A_341	1a49	A	OXLOXALATE ION	M - 359
1a49_A_341	1a49	A	ATPADENOSINE-5'-TRIPHOSPHATE	M - 359
1aqf_A_57	1aqf	A	PEQL-PHOSPHOLACTATE	R - 72
1aqf_A_57	1aqf	A	PEQL-PHOSPHOLACTATE	N - 74
1aqf_A_222	1aqf	A	PEQL-PHOSPHOLACTATE	S - 242
1aqf_A_222	1aqf	A	MGMAGNESIUM ION	S - 242
1aqf_A_222	1aqf	A	PEQL-PHOSPHOLACTATE	F - 243
1aqf_A_222	1aqf	A	MGMAGNESIUM ION	F - 243
1aqf_A_341	1aqf	A	PEQL-PHOSPHOLACTATE	M - 359
1pkn_*_57	1pkn	*	PYRPYRUVIC ACID	R - 72
1pkn_*_341	1pkn	*	PYRPYRUVIC ACID	M - 359
1qpg_*_37	1qpg	*	3PG3-PHOSPHOGLYCERIC ACID	R - 38
1uky_*_78	1uky	*	ADPADENOSINE-5'-DIPHOSPHATE	T - 81
1uky_*_78	1uky	*	ADPADENOSINE-5'-DIPHOSPHATE	D - 103
1ukz_*_78	1ukz	*	AMPADENOSINE MONOPHOSPHATE	T - 81
1ukz_*_78	1ukz	*	ADPADENOSINE-5'-DIPHOSPHATE	D - 103
1ukz_*_78	1ukz	*	AMPADENOSINE MONOPHOSPHATE	D - 103

PDB Site Annotated loops in this subclass

Loop	PDB	Chain	Site	Residue
3bif_A_96	3bif	A	S2WALKER-B MOTIF (ZZZZD, Z=HYDROPHOBIC), PART OF THE CLASSICAL MONONUCLEOTIDE BINDING MOTIF. ASP 128 SERVES AS A LIGAND TO THE MG OF MG-ATP.	V - 124
3bif_A_96	3bif	A	S2WALKER-B MOTIF (ZZZZD, Z=HYDROPHOBIC), PART OF THE CLASSICAL MONONUCLEOTIDE BINDING MOTIF. ASP 128 SERVES AS A LIGAND TO THE MG OF MG-ATP.	D - 128

Bibliographic annotations

Loop	PDB	Chain	Annotation	Residue
1a3w_A_34	1a3w RefM.S.JURICA,A.MESECAR,P.J.HEATH,W.SHI,T.NOWAK,B.L.STODDARD. THE ALLOSTERIC REGULATION OF PYRUVATE KINASE BY FRUCTOSE-1,6-BISPHOSPHATE STRUCTURE (LONDON) v.6;195,1998	A	PHOSPHOGLYCERATE BINDING RESIDUE	R - 49
1a49_A_57	1a49 RefT.M.LARSEN,M.M.BENNING,I.RAYMENT,G.H.REED. STRUCTURE OF THE BIS(MG2+)-ATP-OXALATE COMPLEX OF THE RABBIT MUSCLE PYRUVATE KINASE AT 2.1 A RESOLUTION: ATP BINDING OVER A BARREL BIOCHEMISTRY v.37;6247,1998	A	ATP BINDING RESIDUE	R - 72
1a49_A_57	1a49 RefT.M.LARSEN,M.M.BENNING,I.RAYMENT,G.H.REED. STRUCTURE OF THE BIS(MG2+)-ATP-OXALATE COMPLEX OF THE RABBIT MUSCLE PYRUVATE KINASE AT 2.1 A RESOLUTION: ATP BINDING OVER A BARREL BIOCHEMISTRY v.37;6247,1998	A	ATP BINDING RESIDUE	N - 74
1aqf_A_57	1aqf RefT.M.LARSEN,M.M.BENNING,G.E.WESENBERG,I.RAYMENT,G.H.REED. LIGAND-INDUCED DOMAIN MOVEMENT IN PYRUVATE KINASE: STRUCTURE OF THE ENZYME FROM RABBIT MUSCLE WITH MG2+, K+, AND L-PHOSPHOLACTATE AT 2.7 A RESOLUTION ARCH.BIOCHEM.BIOPHYS. v.345;199,1997	A	LACTATE BINDING RESIDUE	R - 72
1aqf_A_57	1aqf RefT.M.LARSEN,M.M.BENNING,G.E.WESENBERG,I.RAYMENT,G.H.REED. LIGAND-INDUCED DOMAIN MOVEMENT IN PYRUVATE KINASE: STRUCTURE OF THE ENZYME FROM RABBIT MUSCLE WITH MG2+, K+, AND L-PHOSPHOLACTATE AT 2.7 A RESOLUTION ARCH.BIOCHEM.BIOPHYS. v.345;199,1997	A	K ION BINDING RESIDUE	N - 74
3bif_A_96	3bif RefM.H.YUEN,X.WANG,H.MIZUGUCHI,K.UYEDA,C.A.HASEMANN. A SWITCH IN THE KINASE DOMAIN OF RAT TESTIS 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE- 2,6-BISPHOSPHATASE BIOCHEMISTRY v.38;12333,1999	A	F6P BINDING RESIDUE	R - 102
3bif_A_96	3bif RefM.H.YUEN,X.WANG,H.MIZUGUCHI,K.UYEDA,C.A.HASEMANN. A SWITCH IN THE KINASE DOMAIN OF RAT TESTIS 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE- 2,6-BISPHOSPHATASE BIOCHEMISTRY v.38;12333,1999	A	Mg-ATP BINDING RESIDUE	D - 128

Clusters included in this Subclass