3GCM

crystal structure of e. coli polynucleotide phosphorylase bound to rna and rnase e

• Total interactions analyzed: 15
• Total true interactions: 9
• Strongest Interaction:
  • Chains: A-D
  • Int. Res.: 74
  • Norm. En. per Res.: -5.0569
• Hub Node: A(4)

All Interactions

Chains	Hydro. Bond Ener. (kJ/mol)	Elec. Ener. (kJ/mol)	VDW. Ener. (kJ/mol)	Tot. Stab. Ener. (kJ/mol)	#int. res.	# Short cont.	#Hydr. int.	#VDW pairs	#salt bridges	#Pot. fav. elec. int	#Pot. unfav. elec. int
A-D	-103.7606	-27.1033	-243.348	-374.2119	74	12	9	9039	2	11	12
A-B	-105.7681	-118.4777	-508.497	-732.7428	178	19	8	20308	11	41	42
A-C	-124.6239	-101.1579	-501.175	-726.9568	176	24	8	20053	10	42	42
A-F	-20.1447	-13.5201	-84.1971	-117.8619	39	9	2	3230	1	3	2
D-B	-46.3571	-7.2729	-96.0936	-149.7236	43	9	2	3503	1	3	2
B-E	-93.0071	-29.9971	-228.557	-351.5612	73	9	9	8550	1	11	11
B-C	-126.537	-97.4323	-492.297	-716.2663	175	26	8	19830	9	41	44
E-C	-23.7052	-16.0132	-61.8663	-101.5846	41	10	2	3091	1	4	3
C-F	-98.0212	-30.2271	-233.451	-361.6993	72	10	9	8641	3	11	11

Interface residues

• A-D: ALA1040D, ALA1041D, ALA1046D, ALA1050D, ALA1052D, ALA1053D, ALA1055D, ALA341A, ALA526A, ALA529A, ALA540A, ALA543A, ARG1056D, ARG319A, ARG325A, ARG330A, ARG336A, ARG345A, ARG530A, ARG545A, ASN524A, ASN542A, ASP317A, ASP322A, ASP328A, ASP452A, GLN1058D, GLN349A, GLN525A, GLN539A, GLU320A, GLU538A, GLY1039D, GLY1042D, GLY1043D, GLY326A, GLY332A, GLY346A, GLY528A, GLY535A, HIS1044D, HIS1048D, HIS1049D, HIS532A, ILE324A, ILE464A, ILE533A, ILE541A, LEU327A, LEU334A, LEU342A, LEU351A, LEU448A, LEU531A, LYS321A, LYS527A, MET323A, MET466A, MET537A, PRO1054D, PRO1057D, PRO1059D, PRO335A, SER1051D, SER340A, SER479A, THR1045D, THR1047D, THR331A, THR337A, THR344A, VAL329A, VAL333A, VAL536A
• A-B: ALA115B, ALA24B, ALA268A, ALA27B, ALA29B, ALA30B, ALA350A, ALA354A, ALA359A, ALA362A, ALA39B, ALA69B, ALA70B, ARG25B, ARG325A, ARG330A, ARG336A, ARG345A, ARG360A, ARG398B, ARG405A, ARG426A, ARG66B, ARG72B, ARG79B, ARG80B, ARG83A, ARG83B, ASN109B, ASN121B, ASN381A, ASN3B, ASN435A, ASN62B, ASP262A, ASP271A, ASP328A, ASP361A, ASP366A, ASP36B, ASP374A, ASP37B, GLN112B, GLN123B, GLN264A, GLN26B, GLN349A, GLN363A, GLN47B, GLN64B, GLU110B, GLU19B, GLU276A, GLU347A, GLU367A, GLU371A, GLU389A, GLU400A, GLU430A, GLU433A, GLU65B, GLU81B, GLU86A, GLY21B, GLY326A, GLY339A, GLY346A, GLY357A, GLY388A, GLY391A, GLY394A, GLY404A, GLY436A, GLY46B, GLY71B, GLY75A, GLY75B, GLY82B, GLY87A, HIS338A, HIS379A, ILE114B, ILE401A, ILE431A, ILE73B, LEU2B, LEU327A, LEU334A, LEU342A, LEU351A, LEU356A, LEU365A, LEU377A, LEU59B, LYS228B, LYS263A, LYS274A, LYS397A, LYS48B, LYS49B, MET1B, MET22B, MET23B, MET32B, MET35B, MET392A, PHE343A, PHE376A, PHE378A, PHE382A, PHE41B, PHE77B, PHE78B, PRO122B, PRO335A, PRO383A, PRO384A, PRO396A, PRO4B, PRO58B, PRO74B, PRO84A, PRO84B, SER119B, SER275A, SER340A, SER34B, SER386A, SER395A, SER429A, SER434A, SER76A, SER76B, SER85A, THR116B, THR28B, THR337A, THR344A, THR348A, THR353A, THR355A, THR358A, THR373A, THR375A, THR38B, THR390A, THR424A, THR432A, THR43B, THR60B, THR67B, TYR267A, TYR380A, TYR385A, TYR423A, TYR63B, TYR68B, VAL111B, VAL113B, VAL117B, VAL118B, VAL120B, VAL124B, VAL272A, VAL329A, VAL333A, VAL352A, VAL364A, VAL387A, VAL393A, VAL40B, VAL425A, VAL427A, VAL428A, VAL42B, VAL44B, VAL45B, VAL61B
• A-C: ALA115A, ALA24A, ALA268C, ALA27A, ALA29A, ALA30A, ALA350C, ALA354C, ALA359C, ALA362C, ALA39A, ALA69A, ALA70A, ARG25A, ARG266C, ARG325C, ARG330C, ARG336C, ARG345C, ARG360C, ARG405C, ARG426C, ARG66A, ARG72A, ARG79A, ARG80A, ARG83A, ARG83C, ASN109A, ASN121A, ASN381C, ASN3A, ASN435C, ASN62A, ASP262C, ASP271C, ASP328C, ASP361C, ASP366C, ASP36A, ASP374C, ASP37A, GLN112A, GLN123A, GLN264C, GLN26A, GLN349C, GLN363C, GLN47A, GLN64A, GLU110A, GLU19A, GLU265C, GLU276C, GLU347C, GLU367C, GLU371C, GLU389C, GLU400C, GLU430C, GLU433C, GLU81A, GLU86C, GLY21A, GLY326C, GLY339C, GLY346C, GLY357C, GLY388C, GLY391C, GLY394C, GLY404C, GLY436C, GLY46A, GLY71A, GLY75A, GLY75C, GLY82A, HIS338C, HIS379C, ILE114A, ILE401C, ILE431C, ILE73A, LEU2A, LEU327C, LEU334C, LEU342C, LEU351C, LEU356C, LEU365C, LEU377C, LEU59A, LYS228A, LYS263C, LYS274C, LYS397C, LYS48A, LYS49A, MET22A, MET23A, MET32A, MET35A, MET392C, PHE343C, PHE376C, PHE378C, PHE382C, PHE41A, PHE77A, PHE78A, PRO122A, PRO335C, PRO383C, PRO384C, PRO396C, PRO4A, PRO58A, PRO74A, PRO84A, PRO84C, SER119A, SER275C, SER340C, SER34A, SER386C, SER395C, SER429C, SER434C, SER76A, SER76C, SER85C, THR116A, THR28A, THR337C, THR344C, THR348C, THR353C, THR355C, THR358C, THR373C, THR375C, THR38A, THR390C, THR424C, THR432C, THR43A, THR60A, THR67A, TYR267C, TYR380C, TYR385C, TYR423C, TYR63A, TYR68A, VAL111A, VAL113A, VAL117A, VAL118A, VAL120A, VAL124A, VAL272C, VAL329C, VAL333C, VAL352C, VAL364C, VAL387C, VAL393C, VAL40A, VAL425C, VAL427C, VAL428C, VAL42A, VAL44A, VAL45A, VAL61A
• A-F: ALA1040F, ALA1041F, ALA1046F, ALA39A, ARG7A, ASN121A, ASN3A, ASP36A, ASP37A, GLU19A, GLY1039F, GLY1042F, GLY1043F, HIS1044F, HIS1049F, HIS14A, ILE5A, LEU18A, LEU2A, LYS8A, MET22A, MET23A, MET32A, MET35A, PHE41A, PRO4A, SER1051F, SER119A, SER34A, THR1045F, THR15A, THR17A, THR20A, THR38A, VAL118A, VAL16A, VAL33A, VAL40A, VAL6A
• D-B: ALA1040D, ALA1041D, ALA1046D, ALA1050D, ALA1052D, ALA1053D, ALA39B, ARG7B, ASN121B, ASN3B, ASP36B, ASP37B, GLU19B, GLY1039D, GLY1042D, GLY1043D, HIS1044D, HIS1049D, ILE5B, LEU18B, LEU2B, LYS8B, MET1B, MET22B, MET23B, MET32B, MET35B, PHE41B, PRO1054D, PRO4B, SER1051D, SER119B, SER34B, THR1045D, THR15B, THR17B, THR20B, THR38B, VAL118B, VAL16B, VAL33B, VAL40B, VAL6B
• B-E: ALA1040E, ALA1041E, ALA1046E, ALA1050E, ALA1052E, ALA1053E, ALA1055E, ALA341B, ALA526B, ALA529B, ALA540B, ALA543B, ARG1056E, ARG319B, ARG325B, ARG330B, ARG336B, ARG345B, ARG530B, ASN524B, ASN542B, ASP317B, ASP322B, ASP328B, ASP452B, GLN1058E, GLN349B, GLN525B, GLN539B, GLU320B, GLU538B, GLY1042E, GLY1043E, GLY326B, GLY332B, GLY346B, GLY528B, GLY535B, HIS1044E, HIS1048E, HIS1049E, HIS532B, ILE324B, ILE464B, ILE533B, ILE541B, LEU327B, LEU334B, LEU342B, LEU351B, LEU448B, LEU531B, LYS321B, LYS527B, MET323B, MET451B, MET537B, PRO1054E, PRO1057E, PRO1059E, PRO335B, PRO544B, SER1051E, SER340B, SER479B, THR1045E, THR1047E, THR331B, THR337B, THR344B, VAL329B, VAL333B, VAL536B
• B-C: ALA115C, ALA24C, ALA268B, ALA27C, ALA29C, ALA30C, ALA350B, ALA354B, ALA359B, ALA362B, ALA39C, ALA69C, ALA70C, ARG25C, ARG325B, ARG330B, ARG336B, ARG345B, ARG360B, ARG405B, ARG426B, ARG66C, ARG72C, ARG79C, ARG80C, ARG83B, ARG83C, ASN109C, ASN121C, ASN381B, ASN3C, ASN435B, ASN62C, ASP262B, ASP271B, ASP328B, ASP361B, ASP366B, ASP36C, ASP374B, ASP37C, GLN112C, GLN123C, GLN264B, GLN26C, GLN349B, GLN363B, GLN47C, GLN64C, GLU110C, GLU19C, GLU276B, GLU347B, GLU367B, GLU371B, GLU389B, GLU400B, GLU430B, GLU433B, GLU81C, GLU86B, GLY21C, GLY326B, GLY339B, GLY346B, GLY357B, GLY388B, GLY391B, GLY394B, GLY404B, GLY436B, GLY46C, GLY71C, GLY75B, GLY75C, GLY82C, GLY87B, HIS338B, HIS379B, ILE114C, ILE401B, ILE431B, ILE73C, LEU2C, LEU327B, LEU334B, LEU342B, LEU351B, LEU356B, LEU365B, LEU377B, LEU59C, LYS228C, LYS263B, LYS397B, LYS48C, LYS49C, MET1C, MET22C, MET23C, MET32C, MET35C, MET392B, PHE343B, PHE376B, PHE378B, PHE382B, PHE41C, PHE77C, PHE78C, PRO122C, PRO335B, PRO383B, PRO384B, PRO396B, PRO4C, PRO58C, PRO74C, PRO84B, PRO84C, SER119C, SER275B, SER340B, SER34C, SER386B, SER395B, SER429B, SER434B, SER76B, SER76C, SER85B, THR116C, THR28C, THR337B, THR344B, THR348B, THR353B, THR355B, THR358B, THR373B, THR375B, THR38C, THR390B, THR424B, THR432B, THR43C, THR60C, THR67C, TYR267B, TYR380B, TYR385B, TYR423B, TYR63C, TYR68C, VAL111C, VAL113C, VAL117C, VAL118C, VAL120C, VAL124C, VAL272B, VAL329B, VAL333B, VAL352B, VAL364B, VAL387B, VAL393B, VAL40C, VAL425B, VAL427B, VAL428B, VAL42C, VAL44C, VAL45C, VAL61C
• E-C: ALA1040E, ALA1041E, ALA1046E, ALA1050E, ALA1052E, ALA1053E, ALA39C, ARG7C, ASN121C, ASN3C, ASP36C, ASP37C, GLU19C, GLY1042E, GLY1043E, HIS1044E, HIS1049E, ILE5C, LEU18C, LYS8C, MET1C, MET22C, MET23C, MET32C, MET35C, PHE41C, PRO1054E, PRO4C, SER1051E, SER119C, SER34C, THR1045E, THR15C, THR17C, THR20C, THR38C, VAL118C, VAL16C, VAL33C, VAL40C, VAL6C
• C-F: ALA1040F, ALA1041F, ALA1046F, ALA1050F, ALA1052F, ALA1053F, ALA1055F, ALA341C, ALA526C, ALA529C, ALA540C, ALA543C, ARG1056F, ARG319C, ARG325C, ARG330C, ARG336C, ARG345C, ARG530C, ASN524C, ASN542C, ASP317C, ASP322C, ASP328C, ASP452C, GLN1058F, GLN349C, GLN525C, GLN539C, GLU320C, GLU538C, GLY1039F, GLY1042F, GLY1043F, GLY326C, GLY332C, GLY346C, GLY528C, GLY535C, HIS1044F, HIS1048F, HIS1049F, HIS532C, ILE324C, ILE464C, ILE533C, ILE541C, LEU327C, LEU334C, LEU342C, LEU351C, LEU448C, LEU531C, LYS321C, LYS527C, MET323C, MET466C, MET537C, PRO1054F, PRO1057F, PRO1059F, PRO335C, SER1051F, SER340C, SER479C, THR1045F, THR1047F, THR331C, THR344C, VAL329C, VAL333C, VAL536C