Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1D8T

CRYSTAL STRUCTURE OF ELONGATION FACTOR, TU (EF-TU-MGGDP) COMPLEXED WITH GE2270A, A THIAZOLYL PEPTIDE ANTIBIOTIC

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0003723	molecular_function	RNA binding
A	0003746	molecular_function	translation elongation factor activity
A	0003924	molecular_function	GTPase activity
A	0005515	molecular_function	protein binding
A	0005525	molecular_function	GTP binding
A	0005737	cellular_component	cytoplasm
A	0005886	cellular_component	plasma membrane
A	0006412	biological_process	translation
A	0006414	biological_process	translational elongation
A	0016020	cellular_component	membrane
A	0016787	molecular_function	hydrolase activity
A	0032045	cellular_component	guanyl-nucleotide exchange factor complex
A	0046677	biological_process	response to antibiotic
A	0046872	molecular_function	metal ion binding
A	0097216	molecular_function	guanosine tetraphosphate binding
B	0000166	molecular_function	nucleotide binding
B	0000287	molecular_function	magnesium ion binding
B	0003723	molecular_function	RNA binding
B	0003746	molecular_function	translation elongation factor activity
B	0003924	molecular_function	GTPase activity
B	0005515	molecular_function	protein binding
B	0005525	molecular_function	GTP binding
B	0005737	cellular_component	cytoplasm
B	0005886	cellular_component	plasma membrane
B	0006412	biological_process	translation
B	0006414	biological_process	translational elongation
B	0016020	cellular_component	membrane
B	0016787	molecular_function	hydrolase activity
B	0032045	cellular_component	guanyl-nucleotide exchange factor complex
B	0046677	biological_process	response to antibiotic
B	0046872	molecular_function	metal ion binding
B	0097216	molecular_function	guanosine tetraphosphate binding
C	0005576	cellular_component	extracellular region
C	0031640	biological_process	killing of cells of another organism
C	0042742	biological_process	defense response to bacterium
D	0005576	cellular_component	extracellular region
D	0031640	biological_process	killing of cells of another organism
D	0042742	biological_process	defense response to bacterium

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 998

Chain	Residue
A	THR25
A	GDP999
A	HOH2018
A	HOH2063
A	HOH2064
A	HOH2218

site_id	AC2
Number of Residues	21
Details	BINDING SITE FOR RESIDUE GDP A 999

Chain	Residue
A	LYS24
A	THR25
A	THR26
A	PHE46
A	ASN135
A	LYS136
A	ASP138
A	MET139
A	SER173
A	ALA174
A	LEU175
A	MG998
A	HOH2017
A	HOH2063
A	HOH2064
A	HOH2217
A	HOH2218
A	HOH2219
A	ASP21
A	HIS22
A	GLY23

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT A 3002

Chain	Residue
A	THR167
A	PRO168
A	ILE169
A	HOH2115
A	ACT3019

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 3003

Chain	Residue
A	ARG123
A	ASP370
A	ALA389

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 3004

Chain	Residue
A	ARG154
A	ASP165
A	SER221
A	ACT3028

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 3005

Chain	Residue
A	GLU152
A	GLU155
A	GLN159
A	HOH2221

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 3006

Chain	Residue
A	THR302
A	LEU362
A	ILE363
A	HOH2172

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 3007

Chain	Residue
A	VAL127
A	ARG373

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 3010

Chain	Residue
A	PRO113
A	HOH2221
A	HOH2222
B	ACT3009

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 3013

Chain	Residue
A	ARG171
A	TRP184
A	HOH2223
A	ACT3023

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 3016

Chain	Residue
A	ILE247
A	GLU287

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 3017

Chain	Residue
A	VAL391
A	LEU392

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT A 3019

Chain	Residue
A	ILE169
A	VAL170
A	ARG171
A	LYS187
A	GLU190
A	ACT3002

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 3020

Chain	Residue
A	GLU6
A	GLY94
A	ALA95

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 3021

Chain	Residue
A	ASP50
A	PRO82
A	HOH2017

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 3022

Chain	Residue
A	SER65
A	HIS66

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACT A 3023

Chain	Residue
A	VAL140
A	ASP141
A	ASP142
A	GLU143
A	LEU146
A	ACT3013
C	BB92

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 3025

Chain	Residue
A	TYR129
A	TYR198
A	HOH2226
A	HOH2227

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 3026

Chain	Residue
A	HIS84
A	ASN355

site_id	CC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 3028

Chain	Residue
A	ILE220
A	SER221
A	ACT3004

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 3030

Chain	Residue
A	TYR39
A	LEU189
A	ALA192
A	ASP196

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG B 998

Chain	Residue
B	HOH2013
B	HOH2140
B	HOH2141
B	THR25
B	ASP50
B	GDP999
B	HOH2006

site_id	CC5
Number of Residues	19
Details	BINDING SITE FOR RESIDUE GDP B 999

Chain	Residue
B	ASP21
B	HIS22
B	GLY23
B	LYS24
B	THR25
B	THR26
B	PHE46
B	ASN135
B	LYS136
B	ASP138
B	MET139
B	SER173
B	ALA174
B	LEU175
B	MG998
B	HOH2004
B	HOH2139
B	HOH2140
B	HOH2141

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT B 3001

Chain	Residue
B	ARG154
B	ILE169
B	ACT3008

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT B 3008

Chain	Residue
B	VAL170
B	ARG171
B	LYS187
B	GLU190
B	ACT3001

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT B 3009

Chain	Residue
A	PRO111
A	ACT3010
B	ARG318
B	HIS319
B	THR320
B	GLU378

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT B 3011

Chain	Residue
A	PHE323
A	GLU348
B	VAL140
B	ASP141
B	ASP142

site_id	DC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT B 3012

Chain	Residue
B	GLU215
B	ARG288
B	TYR331
B	ARG333
B	HOH2087

site_id	DC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT B 3014

Chain	Residue
B	HIS84
B	GLY353
B	ASN355

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT B 3015

Chain	Residue
B	GLY41
B	ALA42
B	GLU68
B	ASP70
B	HOH2008

site_id	DC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT B 3018

Chain	Residue
B	ASP166

site_id	DC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT B 3024

Chain	Residue
B	GLU201
B	HOH2144

site_id	DC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT B 3027

Chain	Residue
B	ASP336

site_id	DC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT B 3029

Chain	Residue
B	TYR39
B	LEU189
B	ASP196
B	HOH2145
B	HOH2146

site_id	DC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NH2 C 15

Chain	Residue
A	GLY222
C	PRO14

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NH2 D 15

Chain	Residue
B	GLY222
D	SER13
D	PRO14

site_id	EC1
Number of Residues	27
Details	BINDING SITE FOR CHAIN C OF THIOCILIN GE2270

Chain	Residue
A	THR73
A	GLU143
A	ALA182
A	GLU215
A	ASP216
A	GLY222
A	ARG223
A	VAL226
A	THR228
A	GLY229
A	ARG230
A	THR256
A	GLY257
A	VAL258
A	GLU259
A	PHE261
A	ARG262
A	ASN273
A	VAL274
A	GLY275
A	LEU277
A	HOH2024
A	HOH2161
A	ACT3023
C	NH215
C	HOH2002
C	HOH2003

site_id	EC2
Number of Residues	25
Details	BINDING SITE FOR CHAIN D OF THIOCILIN GE2270

Chain	Residue
B	PRO72
B	THR73
B	GLU143
B	GLU215
B	ASP216
B	PHE218
B	ARG223
B	VAL226
B	THR228
B	ARG230
B	THR256
B	GLY257
B	VAL258
B	GLU259
B	PHE261
B	ARG262
B	LEU264
B	ASN273
B	VAL274
B	GLY275
B	LEU277
B	HOH2097
B	HOH2099
D	NH215
D	HOH2001

Functional Information from PROSITE/UniProt

site_id	PS00301
Number of Residues	16
Details	G_TR_1 Translational (tr)-type guanine nucleotide-binding (G) domain signature. DNapeEKaRGITIntS

Chain	Residue	Details
A	ASP50-SER65

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	388
Details	Domain: {"description":"tr-type G"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	14
Details	Region: {"description":"G1","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Region: {"description":"G2","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Region: {"description":"G3","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Region: {"description":"G4","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Region: {"description":"G5","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	28
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29546243","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5MI3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5OPD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	10
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"21151122","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"2022614","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"389663","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"6997043","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7021545","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19150849","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24141193","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8416965","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PubMed","id":"29546243","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5OPD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	a catalytic site defined by CSA, PubMed 20434456

Chain	Residue	Details
A	ASP21

site_id	CSA2
Number of Residues	1
Details	a catalytic site defined by CSA, PubMed 20434456

Chain	Residue	Details
B	ASP21

site_id	MCSA1
Number of Residues	4
Details	M-CSA 535

Chain	Residue	Details
A	ASP21	electrostatic stabiliser
A	LYS24	electrostatic stabiliser
A	THR25	metal ligand
A	HIS84	electrostatic stabiliser

site_id	MCSA2
Number of Residues	4
Details	M-CSA 535

Chain	Residue	Details
B	ASP21	electrostatic stabiliser
B	LYS24	electrostatic stabiliser
B	THR25	metal ligand
B	HIS84	electrostatic stabiliser

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)