1IB6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF R153C E. COLI MALATE DEHYDROGENASE

Authors :   J. K. Bell, H. P. Yennawar, S. K. Wright, J. R. Thompson, R. E. Viola, L. J. Banaszak

Date :   27 Mar 01 (Deposition) - 19 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Oxidoreductase, Dehydrogenase, Malate Dehydrogenase, Substrate Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. K. Bell, H. P. Yennawar, S. K. Wright, J. R. Thompson, R. E. Viola, L. J. Banaszak
Structural Analyses Of A Malate Dehydrogenase With A Variable Active Site
J. Biol. Chem. V. 276 31156 2001
PubMed-ID: 11389141 | Reference-DOI: 10.1074/JBC.M100902200
(for further references see the PDB file header)

Molecule 1 - MALATE DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEM6
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MDH
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:81 , ARG A:87 , ASN A:119 , HIS A:177 , GLY A:210 , NAD A:313 , HOH A:344 , HOH A:353	BINDING SITE FOR RESIDUE SO4 A 316
2	AC2	SOFTWARE	ARG A:81 , ASP A:86 , ARG A:87 , SER A:88 , SER A:178 , GLY A:179	BINDING SITE FOR RESIDUE SO4 A 317
3	AC3	SOFTWARE	ARG C:81 , ARG C:87 , ASN C:119 , HIS C:177 , GLY C:210 , NAD C:314 , HOH C:473	BINDING SITE FOR RESIDUE SO4 C 318
4	AC4	SOFTWARE	ARG C:81 , ASP C:86 , ARG C:87 , SER C:88 , SER C:178 , GLY C:179 , HOH C:467	BINDING SITE FOR RESIDUE SO4 C 319
5	AC5	SOFTWARE	ARG D:81 , ARG D:87 , ASN D:119 , HIS D:177 , GLY D:210 , NAD D:315 , HOH D:531 , HOH D:532 , HOH D:533	BINDING SITE FOR RESIDUE SO4 D 320
6	AC6	SOFTWARE	ASP D:86 , ARG D:87 , SER D:88 , SER D:178 , GLY D:179	BINDING SITE FOR RESIDUE SO4 D 321
7	AC7	SOFTWARE	GLY A:7 , ALA A:9 , GLY A:10 , GLY A:11 , ILE A:12 , TYR A:33 , ASP A:34 , ILE A:35 , SER A:76 , ALA A:77 , GLY A:78 , VAL A:79 , ALA A:80 , LEU A:90 , ASN A:94 , ILE A:97 , ILE A:117 , THR A:118 , ASN A:119 , VAL A:146 , LEU A:149 , HIS A:177 , ALA A:223 , MET A:227 , SO4 A:316 , HOH A:343 , HOH A:345 , HOH A:348 , HOH A:349 , HOH A:396 , HOH A:397	BINDING SITE FOR RESIDUE NAD A 313
8	AC8	SOFTWARE	ALA C:9 , GLY C:10 , GLY C:11 , ILE C:12 , TYR C:33 , ASP C:34 , ILE C:35 , SER C:76 , ALA C:77 , GLY C:78 , VAL C:79 , ALA C:80 , ASN C:94 , ILE C:97 , ILE C:117 , ASN C:119 , VAL C:121 , VAL C:146 , HIS C:177 , ALA C:223 , THR C:224 , MET C:227 , SO4 C:318 , HOH C:473 , HOH C:474 , HOH C:475 , HOH C:479 , HOH C:480	BINDING SITE FOR RESIDUE NAD C 314
9	AC9	SOFTWARE	GLY D:7 , ALA D:9 , GLY D:10 , GLY D:11 , ILE D:12 , TYR D:33 , ASP D:34 , SER D:76 , ALA D:77 , GLY D:78 , VAL D:79 , LEU D:90 , ASN D:94 , ILE D:97 , ILE D:117 , ASN D:119 , VAL D:121 , VAL D:146 , HIS D:177 , ALA D:223 , THR D:224 , MET D:227 , SO4 D:320 , HOH D:529 , HOH D:530 , HOH D:531 , HOH D:549 , HOH D:563 , HOH D:564 , HOH D:577	BINDING SITE FOR RESIDUE NAD D 315

(no "SS Bond" information available for 1IB6)

Asymmetric Unit

No.	Residues
1	Asn A:119	-	Pro A:120
2	Asn B:119	-	Pro B:120
3	Asn C:119	-	Pro C:120
4	Asn D:119	-	Pro D:120

Asymmetric Unit (11, 44)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_MDH_ECOLI_001 *	D	71	N	MDH_ECOLI	---	---	A/B/C/D	D	71	N
02	UniProt	VAR_MDH_ECOLI_002 *	A	106	S	MDH_ECOLI	---	---	A/B/C/D	A	106	S
03	UniProt	VAR_MDH_ECOLI_003 *	A	209	P	MDH_ECOLI	---	---	A/B/C/D	A	209	P
04	UniProt	VAR_MDH_ECOLI_004 *	A	218	R	MDH_ECOLI	---	---	A/B/C/D	A	218	R
05	UniProt	VAR_MDH_ECOLI_005 *	A	232	T	MDH_ECOLI	---	---	A/B/C/D	A	232	T
06	UniProt	VAR_MDH_ECOLI_006 *	V	249	I	MDH_ECOLI	---	---	A/B/C/D	V	249	I
07	UniProt	VAR_MDH_ECOLI_007 *	Q	289	K	MDH_ECOLI	---	---	A/B/C/D	Q	289	K
08	UniProt	VAR_MDH_ECOLI_008 *	N	290	S	MDH_ECOLI	---	---	A/B/C/D	N	290	S
09	UniProt	VAR_MDH_ECOLI_009 *	A	291	S	MDH_ECOLI	---	---	A/B/C/D	A	291	S
10	UniProt	VAR_MDH_ECOLI_010 *	G	294	A	MDH_ECOLI	---	---	A/B/C/D	G	294	A
11	UniProt	VAR_MDH_ECOLI_011 *	D	297	N	MDH_ECOLI	---	---	A/B/C/D	D	297	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (11, 22)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_MDH_ECOLI_001 *	D	71	N	MDH_ECOLI	---	---	A/B	D	71	N
02	UniProt	VAR_MDH_ECOLI_002 *	A	106	S	MDH_ECOLI	---	---	A/B	A	106	S
03	UniProt	VAR_MDH_ECOLI_003 *	A	209	P	MDH_ECOLI	---	---	A/B	A	209	P
04	UniProt	VAR_MDH_ECOLI_004 *	A	218	R	MDH_ECOLI	---	---	A/B	A	218	R
05	UniProt	VAR_MDH_ECOLI_005 *	A	232	T	MDH_ECOLI	---	---	A/B	A	232	T
06	UniProt	VAR_MDH_ECOLI_006 *	V	249	I	MDH_ECOLI	---	---	A/B	V	249	I
07	UniProt	VAR_MDH_ECOLI_007 *	Q	289	K	MDH_ECOLI	---	---	A/B	Q	289	K
08	UniProt	VAR_MDH_ECOLI_008 *	N	290	S	MDH_ECOLI	---	---	A/B	N	290	S
09	UniProt	VAR_MDH_ECOLI_009 *	A	291	S	MDH_ECOLI	---	---	A/B	A	291	S
10	UniProt	VAR_MDH_ECOLI_010 *	G	294	A	MDH_ECOLI	---	---	A/B	G	294	A
11	UniProt	VAR_MDH_ECOLI_011 *	D	297	N	MDH_ECOLI	---	---	A/B	D	297	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (11, 22)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_MDH_ECOLI_001 *	D	71	N	MDH_ECOLI	---	---	C/D	D	71	N
02	UniProt	VAR_MDH_ECOLI_002 *	A	106	S	MDH_ECOLI	---	---	C/D	A	106	S
03	UniProt	VAR_MDH_ECOLI_003 *	A	209	P	MDH_ECOLI	---	---	C/D	A	209	P
04	UniProt	VAR_MDH_ECOLI_004 *	A	218	R	MDH_ECOLI	---	---	C/D	A	218	R
05	UniProt	VAR_MDH_ECOLI_005 *	A	232	T	MDH_ECOLI	---	---	C/D	A	232	T
06	UniProt	VAR_MDH_ECOLI_006 *	V	249	I	MDH_ECOLI	---	---	C/D	V	249	I
07	UniProt	VAR_MDH_ECOLI_007 *	Q	289	K	MDH_ECOLI	---	---	C/D	Q	289	K
08	UniProt	VAR_MDH_ECOLI_008 *	N	290	S	MDH_ECOLI	---	---	C/D	N	290	S
09	UniProt	VAR_MDH_ECOLI_009 *	A	291	S	MDH_ECOLI	---	---	C/D	A	291	S
10	UniProt	VAR_MDH_ECOLI_010 *	G	294	A	MDH_ECOLI	---	---	C/D	G	294	A
11	UniProt	VAR_MDH_ECOLI_011 *	D	297	N	MDH_ECOLI	---	---	C/D	D	297	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDH_ECOLI	146-158	4	A:146-158 B:146-158 C:146-158 D:146-158

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDH_ECOLI	146-158	2	A:146-158 B:146-158 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MDH	PS00068	Malate dehydrogenase active site signature.	MDH_ECOLI	146-158	2	- - C:146-158 D:146-158

(no "Exon" information available for 1IB6)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:312
 aligned with MDH_ECOLI | P61889 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
            MDH_ECOLI     1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK 312
               SCOP domains d1ib6a1 A:1-145 Malate dehydrogenase                                                                                                             d1ib6a2 A:146-312 Malate dehydrogenase                                                                                                                                  SCOP domains
               CATH domains 1ib6A01 A:1-146 NAD(P)-binding Rossmann-like Domain                                                                                               1ib6A02 A:147-312 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eeeee....hhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhhh.hhhhh...eee......eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------N----------------------------------S------------------------------------------------------------------------------------------------------P--------R-------------T----------------I---------------------------------------KSS--A--N--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ib6 A   1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIICSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGQEFVNK 312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with MDH_ECOLI | P61889 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
            MDH_ECOLI     1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK 312
               SCOP domains d1ib6b1 B:1-145 Malate dehydrogenase                                                                                                             d1ib6b2 B:146-312 Malate dehydrogenase                                                                                                                                  SCOP domains
               CATH domains 1ib6B01 B:1-146 NAD(P)-binding Rossmann-like Domain                                                                                               1ib6B02 B:147-312 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.....eeeee....hhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh...hhh.eee.hhhhhhhhhhhhhhhhh.hhhhh...eee..hhh.eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------N----------------------------------S------------------------------------------------------------------------------------------------------P--------R-------------T----------------I---------------------------------------KSS--A--N--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ib6 B   1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIICSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGQEFVNK 312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain C from PDB  Type:PROTEIN  Length:312
 aligned with MDH_ECOLI | P61889 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
            MDH_ECOLI     1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK 312
               SCOP domains d1ib6c1 C:1-145 Malate dehydrogenase                                                                                                             d1ib6c2 C:146-312 Malate dehydrogenase                                                                                                                                  SCOP domains
               CATH domains 1ib6C01 C:1-146 NAD(P)-binding Rossmann-like Domain                                                                                               1ib6C02 C:147-312 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eeeee....hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhh..hhhhh...eee......eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------N----------------------------------S------------------------------------------------------------------------------------------------------P--------R-------------T----------------I---------------------------------------KSS--A--N--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ib6 C   1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIICSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGQEFVNK 312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain D from PDB  Type:PROTEIN  Length:312
 aligned with MDH_ECOLI | P61889 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
            MDH_ECOLI     1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIIRSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGEEFVNK 312
               SCOP domains d1ib6d1 D:1-145 Malate dehydrogenase                                                                                                             d1ib6d2 D:146-312 Malate dehydrogenase                                                                                                                                  SCOP domains
               CATH domains 1ib6D01 D:1-146 NAD(P)-binding Rossmann-like Domain                                                                                               1ib6D02 D:147-312 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhh.....eeeeee....hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhh..hhhhh...eee......eee.hhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeeeeee..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------N----------------------------------S------------------------------------------------------------------------------------------------------P--------R-------------T----------------I---------------------------------------KSS--A--N--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------MDH          ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ib6 D   1 MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIPTAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKNLVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLDIICSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVADLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLKKDIALGQEFVNK 312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: LDH C-terminal domain-like (172)

Superfamily: LDH C-terminal domain-like (172)

Family: Lactate & malate dehydrogenases, C-terminal domain (125)

Protein domain: Malate dehydrogenase (37)

Escherichia coli [TaxId: 562] (4)

1a	d1ib6a2	A:146-312
1b	d1ib6b2	B:146-312
1c	d1ib6c2	C:146-312
1d	d1ib6d2	D:146-312

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: LDH N-terminal domain-like (117)

Protein domain: Malate dehydrogenase (39)

Escherichia coli [TaxId: 562] (4)

2a	d1ib6a1	A:1-145
2b	d1ib6b1	B:1-145
2c	d1ib6c1	C:1-145
2d	d1ib6d1	D:1-145

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Escherichia coli. Organism_taxid: 562. (48)

1a	1ib6A01	A:1-146
1b	1ib6B01	B:1-146
1c	1ib6C01	C:1-146
1d	1ib6D01	D:1-146

Architecture: Alpha-Beta Complex (3881)

Topology: L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 (116)

Homologous Superfamily: L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2 (116)

Escherichia coli. Organism_taxid: 562. (2)

2a	1ib6A02	A:147-312
2b	1ib6B02	B:147-312
2c	1ib6C02	C:147-312
2d	1ib6D02	D:147-312

(no "Pfam Domain" information available for 1IB6)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MDH_ECOLI | P61889)

molecular function
	GO:0030060	L-malate dehydrogenase activity	Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016615	malate dehydrogenase activity	Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0009061	anaerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0006113	fermentation	The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP).
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	GO:0006108	malate metabolic process	The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:119 - Pro A:120	[ RasMol ]
		Asn B:119 - Pro B:120	[ RasMol ]
		Asn C:119 - Pro C:120	[ RasMol ]
		Asn D:119 - Pro D:120	[ RasMol ]

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	1ib6
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	1.1.1.37
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	MDH_ECOLI \| P61889	:	1cme 1emd 1ie3 2cmd 2pwz 3hhp 5kka

(no "Related Entries Specified in the PDB File" available for 1IB6)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (11, 44)

PROSITE Motifs (1, 4)

Exons (0, 0)

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SCOP Domains (2, 8)

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