1XP4 - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PEPTIDOGLYCAN SYNTHESIS REGULATORY FACTOR (PBP3) FROM STREPTOCOCCUS PNEUMONIAE

Authors :   C. Morlot, L. Pernot, A. Le Gouellec, A. M. Di Guilmi, T. Vernet, O. Dideberg, A. Dessen

Date :   08 Oct 04 (Deposition) - 09 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Five-Stranded Antiparallel Beta-Sheet, Omega-Like Loop, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Morlot, L. Pernot, A. Le Gouellec, A. M. Di Guilmi, T. Vernet, O. Dideberg, A. Dessen
Crystal Structure Of A Peptidoglycan Synthesis Regulatory Factor (Pbp3) From Streptococcus Pneumoniae
J. Biol. Chem. V. 280 15984 2005
PubMed-ID: 15596446 | Reference-DOI: 10.1074/JBC.M408446200
(for further references see the PDB file header)

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
	Chains	:	A, B, C, D
	EC Number	:	3.4.16.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	MC1061
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 16-394
	Gene	:	DACA
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE R6
	Organism Taxid	:	171101
	Strain	:	ATCC BAA-255 / R6
	Synonym	:	D-ALA,D-ALA-CARBOXYPEPTIDASE PBP3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 56)

No.	Name	Count	Type	Full Name
1	IOD	16	Ligand/Ion	IODIDE ION
2	MSE	36	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	IOD	4	Ligand/Ion	IODIDE ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	IOD	4	Ligand/Ion	IODIDE ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 14)

No.	Name	Count	Type	Full Name
1	IOD	4	Ligand/Ion	IODIDE ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 14)

No.	Name	Count	Type	Full Name
1	IOD	4	Ligand/Ion	IODIDE ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:56 , SER A:119 , LYS A:239 , THR A:240 , THR A:242 , HOH A:597	BINDING SITE FOR RESIDUE SO4 A 464
02	AC2	SOFTWARE	SER B:56 , SER B:119 , THR B:240 , THR B:242 , HOH B:495	BINDING SITE FOR RESIDUE SO4 B 465
03	AC3	SOFTWARE	SER C:56 , SER C:97 , SER C:119 , THR C:221 , THR C:240 , GLY C:241 , THR C:242	BINDING SITE FOR RESIDUE SO4 C 466
04	AC4	SOFTWARE	SER D:56 , SER D:119 , LYS D:239 , THR D:240 , THR D:242 , HOH D:585	BINDING SITE FOR RESIDUE SO4 D 467
05	AC5	SOFTWARE	GLN A:374	BINDING SITE FOR RESIDUE IOD A 468
06	AC6	SOFTWARE	PRO A:275	BINDING SITE FOR RESIDUE IOD A 470
07	AC7	SOFTWARE	GLN A:201	BINDING SITE FOR RESIDUE IOD A 471
08	AC8	SOFTWARE	GLU B:45 , GLN B:374	BINDING SITE FOR RESIDUE IOD B 472
09	AC9	SOFTWARE	PHE B:279	BINDING SITE FOR RESIDUE IOD B 474
10	BC1	SOFTWARE	GLN C:374	BINDING SITE FOR RESIDUE IOD C 476
11	BC2	SOFTWARE	TYR C:223 , PRO C:275	BINDING SITE FOR RESIDUE IOD C 478
12	BC3	SOFTWARE	GLU D:45 , GLN D:374	BINDING SITE FOR RESIDUE IOD D 481
13	BC4	SOFTWARE	TYR D:276	BINDING SITE FOR RESIDUE IOD D 482

(no "SS Bond" information available for 1XP4)

Asymmetric Unit

No.	Residues
1	Gly A:237	-	Leu A:238
2	Ala A:353	-	Pro A:354
3	Gly C:237	-	Leu C:238

(no "SAP(SNP)/Variant" information available for 1XP4)

(no "PROSITE Motif" information available for 1XP4)

(no "Exon" information available for 1XP4)

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:369
 aligned with Q8DQ99_STRR6 | Q8DQ99 from UniProtKB/TrEMBL  Length:413

    Alignment length:369
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384         
         Q8DQ99_STRR6    25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPMEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDMMRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGMTITSTNYMLEGMPAYRGGFDGLKTGTTDKAGESFVGTTVEKGMRVITVVLNADHQDNNPYARFTATSSLMDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIERVGNQSSQSVQFTPDSKAIPAPLEAGTVVGHLTYEDKDLIGQGYITTERPSFEMVADKKIE 393
               SCOP domains d1xp4a2 A:25-293 D,D-carboxypeptidase DacA, N-terminal domain                                                                                                                                                                                                                d1xp4a1 A:294-386 D,D-carboxypeptidase DacA, C-terminal domain                               ------- SCOP domains
               CATH domains 1xp4A01 A:25-293 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                     1xp4A02 A:294-393 Peptidoglycan synthesis regulatory factor (PBP3), Domain 2                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeeeee.....ee.hhhhhhhhhhhhhhhhhhh......eee.hhhhhhh..............eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..............eehhhhhhhhhhhhhhhh..hhhhhh..eeee..eeee...............eeeeeeeee...eeeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhheeeeeee......................ee....eeeeee..........................eeeeee.................eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xp4 A  25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPmEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDmmRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGmTITSTNYmLEGmPAYRGGFDGLKTGTTDKAGESFVGTTVEKGmRVITVVLNADHQDNNPYARFTATSSLmDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIERVGNQSSQSVQFTPDSKAIPAPLEAGTVVGHLTYEDKDLIGQGYITTERPSFEmVADKKIE 393
                                    34        44        54        64        74        84        94      |104       114       124       134      |144       154       164       174       184       194       204       214 |     224   |   234       244       254    |  264       274       284 |     294       304       314       324       334       344       354       364       374       384 |       
                                                                                                      101-MSE                                 141-MSE                                                                    216-MSE 224-MSE                            259-MSE                    286-MSE                                                                                             386-MSE   
                                                                                                                                               142-MSE                                                                               228-MSE

Chain B from PDB  Type:PROTEIN  Length:339
 aligned with Q8DQ99_STRR6 | Q8DQ99 from UniProtKB/TrEMBL  Length:413

    Alignment length:367
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       
         Q8DQ99_STRR6    25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPMEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDMMRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGMTITSTNYMLEGMPAYRGGFDGLKTGTTDKAGESFVGTTVEKGMRVITVVLNADHQDNNPYARFTATSSLMDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIERVGNQSSQSVQFTPDSKAIPAPLEAGTVVGHLTYEDKDLIGQGYITTERPSFEMVADKK 391
               SCOP domains d1xp4b2 B:25-293 D,D-carboxypeptidase DacA, N-terminal domain                                                                                                                                                                                                                d1xp4b1 B:294-3            86 D,D-carboxypeptidase Dac            A, C-terminal domain       ----- SCOP domains
               CATH domains 1xp4B01 B:25-293 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                     ---------------            ---------------------------            -------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......eee.hhhhhhh..............eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh.............eehhhhhhhhhhhhhhhh.hhhhhhh..eeee..eeee...................eeee.....eeeeeeeee..eeeeeeee....----.hhhhhhhhhhhhhhhh.eeeeeee.........------------.......eeeeee..............------------..eeee.................eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xp4 B  25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPmEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDmmRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGmTITSTNYmLEGmPAYRGGFDGLKTGTTDKAGESFVGTTVEKGmRVITVVLNADH----PYARFTATSSLmDYISSTFTLRKIVQQGDAYQDS------------IAVAPEDIYLIERVGNQSSQSVQFTPD------------VVGHLTYEDKDLIGQGYITTERPSFEmVADKK 391
                                    34        44        54        64        74        84        94      |104       114       124       134      |144       154       164       174       184       194       204       214 |     224   |   234       244       254    |  264     |   -|      284 |     294       304   |     -      |324       334       344  |      -     | 364       374       384 |     
                                                                                                      101-MSE                                 141-MSE                                                                    216-MSE 224-MSE                            259-MSE    270  275        286-MSE               308          321                       347          360                       386-MSE 
                                                                                                                                               142-MSE                                                                               228-MSE

Chain C from PDB  Type:PROTEIN  Length:359
 aligned with Q8DQ99_STRR6 | Q8DQ99 from UniProtKB/TrEMBL  Length:413

    Alignment length:368
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384        
         Q8DQ99_STRR6    25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPMEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDMMRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGMTITSTNYMLEGMPAYRGGFDGLKTGTTDKAGESFVGTTVEKGMRVITVVLNADHQDNNPYARFTATSSLMDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIERVGNQSSQSVQFTPDSKAIPAPLEAGTVVGHLTYEDKDLIGQGYITTERPSFEMVADKKI 392
               SCOP domains d1xp4c2 C:25-293 D,D-carboxypeptidase DacA, N-terminal domain                                                                                                                                                                                                                d1xp4c1 C:294-386 D,D-carboxypeptidase DacA   , C-termi      nal domain                      ------ SCOP domains
               CATH domains 1xp4C01 C:25-293 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                     1xp4C02 C:294-392 Peptidoglycan synthesis r   egulatory       factor (PBP3), Domain 2               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeeeee.....ee.hhhhhhhhhhhhhhhhhhh......eee.hhhhhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..............eehhhhhhhhhhhhhhhh..hhhhhh..eeee..eeee..................eeeeee...eeeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhheeeeeee....eeeeeee.........eeee....eeeeee...---.........------.....eeeeee.................eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xp4 C  25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPmEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDmmRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGmTITSTNYmLEGmPAYRGGFDGLKTGTTDKAGESFVGTTVEKGmRVITVVLNADHQDNNPYARFTATSSLmDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIERVGN---QSVQFTPDS------LEAGTVVGHLTYEDKDLIGQGYITTERPSFEmVADKKI 392
                                    34        44        54        64        74        84        94      |104       114       124       134      |144       154       164       174       184       194       204       214 |     224   |   234       244       254    |  264       274       284 |     294       304       314       324       334 |   | 344   |     -|      364       374       384 |      
                                                                                                      101-MSE                                 141-MSE                                                                    216-MSE 224-MSE                            259-MSE                    286-MSE                                           336 340     348    355                            386-MSE  
                                                                                                                                               142-MSE                                                                               228-MSE

Chain D from PDB  Type:PROTEIN  Length:321
 aligned with Q8DQ99_STRR6 | Q8DQ99 from UniProtKB/TrEMBL  Length:413

    Alignment length:362
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384  
         Q8DQ99_STRR6    25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPMEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDMMRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGMTITSTNYMLEGMPAYRGGFDGLKTGTTDKAGESFVGTTVEKGMRVITVVLNADHQDNNPYARFTATSSLMDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIERVGNQSSQSVQFTPDSKAIPAPLEAGTVVGHLTYEDKDLIGQGYITTERPSFEM 386
               SCOP domains d1xp4d2 D:25-293 D,D-carboxypeptidase DacA, N-terminal domain                                                                                                                                                                                                                d1xp4d1 D:294-38            6 D,D-carboxy     peptidas               e DacA, C-terminal domai SCOP domains
               CATH domains 1xp4D01 D:25-293 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                     ----------------            -------------     --------               ------------------------ CATH domains
           Pfam domains (1) Peptidase_S11-1xp4D01 D:25-270                                                                                                                                                                                                                            ------------------PBP5_C-1xp4D05 D:            293-386                                                           Pfam domains (1)
           Pfam domains (2) Peptidase_S11-1xp4D02 D:25-270                                                                                                                                                                                                                            ------------------PBP5_C-1xp4D06 D:            293-386                                                           Pfam domains (2)
           Pfam domains (3) Peptidase_S11-1xp4D03 D:25-270                                                                                                                                                                                                                            ------------------PBP5_C-1xp4D07 D:            293-386                                                           Pfam domains (3)
           Pfam domains (4) Peptidase_S11-1xp4D04 D:25-270                                                                                                                                                                                                                            ------------------PBP5_C-1xp4D08 D:            293-386                                                           Pfam domains (4)
         Sec.struct. author ....eeeeeeee.....eeeee.....ee.hhhhhhhhhhhhhhhhhhh......eee.hhhhhh....-----......eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh.............eehhhhhhhhhhhhhhhh.hhhhhhh..eeee..eeee...................eeeee...eeeeeeeeee..eeeeeeeeee..----...hhhhhhhhhhhhhhheeeeeee..........------------......eeeeee.-----........---------------.ee.................ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xp4 D  25 FTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTN-----IPmEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDmmRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGmTITSTNYmLEGmPAYRGGFDGLKTGTTDKAGESFVGTTVEKGmRVITVVLNADH----PYARFTATSSLmDYISSTFTLRKIVQQGDAYQDSK------------AVAPEDIYLIERV-----QSVQFTPD---------------HLTYEDKDLIGQGYITTERPSFEm 386
                                    34        44        54        64        74        84        |-    | |104       114       124       134      |144       154       164       174       184       194       204       214 |     224   |   234       244       254    |  264     |   -|      284 |     294       304    |    -       324       334     | 344  |      -       364       374       384 |
                                                                                               93    99 |                                     141-MSE                                                                    216-MSE 224-MSE                            259-MSE    270  275        286-MSE                309          322         334   340    347             363                    386-MSE
                                                                                                      101-MSE                                  142-MSE                                                                               228-MSE

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Peptidase_S11 (12)

Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (1)

1a	Peptidase_S11-1xp4D01	D:25-270
1b	Peptidase_S11-1xp4D02	D:25-270
1c	Peptidase_S11-1xp4D03	D:25-270
1d	Peptidase_S11-1xp4D04	D:25-270

Clan: no clan defined [family: PBP5_C] (10)

Family: PBP5_C (10)

Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (1)

2a	PBP5_C-1xp4D05	D:293-386
2b	PBP5_C-1xp4D06	D:293-386
2c	PBP5_C-1xp4D07	D:293-386
2d	PBP5_C-1xp4D08	D:293-386

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q8DQ99_STRR6 | Q8DQ99)

molecular function
	GO:0004180	carboxypeptidase activity	Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
biological process
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		IOD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:353 - Pro A:354	[ RasMol ]
		Gly A:237 - Leu A:238	[ RasMol ]
		Gly C:237 - Leu C:238	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1xp4
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q8DQ99_STRR6 \| Q8DQ99
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	3.4.16.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q8DQ99_STRR6 \| Q8DQ99
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1XP4)

(no "Related Entries Specified in the PDB File" available for 1XP4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 56)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (2, 6)

Pfam Domains (2, 8)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File