1NMA - JenaLib

Title :   N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRICAL FREE-ENERGY CALCULATIONS CAPTURE SPECIFICITY TRENDS OBSERVED WITH MUTANT BINDING DATA

Authors :   W. R. Tulip, J. N. Varghese, P. M. Colman

Date :   06 May 94 (Deposition) - 15 Sep 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : H,L,N
Biol. Unit 1: H,L,N  (4x)

Keywords :   Complex (Hydrolase-Immunoglobulin), Complex (Hydrolase- Immunoglobulin) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. R. Tulip, V. R. Harley, R. G. Webster, J. Novotny
N9 Neuraminidase Complexes With Antibodies Nc41 And Nc10: Empirical Free Energy Calculations Capture Specificity Trends Observed With Mutant Binding Data.
Biochemistry V. 33 7986 1994
PubMed-ID: 7517697 | Reference-DOI: 10.1021/BI00192A002
(for further references see the PDB file header)

Compounds

Molecule 1 - N9 NEURAMINIDASE
	Chains	:	N
	EC Number	:	3.2.1.18
	Mutation	:	YES
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	11320

Molecule 2 - FAB NC10
	Chains	:	L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	RESOLUTION OF 3.0 ANGSTROMS
	Other Details - Source	:	ISOLATED FROM MONOCLONAL MURINE ANTIBODY

Molecule 3 - FAB NC10
	Chains	:	H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	RESOLUTION OF 3.0 ANGSTROMS
	Other Details - Source	:	ISOLATED FROM MONOCLONAL MURINE ANTIBODY

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 28)

No.	Name	Count	Type	Full Name
1	BMA	4	Ligand/Ion	BETA-D-MANNOSE
2	MAN	12	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN N:200 , LEU N:453 , GLY N:454 , GLN N:455 , NAG N:470B	BINDING SITE FOR RESIDUE NAG N 469A
2	AC2	SOFTWARE	GLN N:392 , GLY N:394 , NAG N:469A , BMA N:471C	BINDING SITE FOR RESIDUE NAG N 470B
3	AC3	SOFTWARE	LEU N:377 , PRO N:390 , GLY N:394 , NAG N:470B , MAN N:472D	BINDING SITE FOR RESIDUE BMA N 471C
4	AC4	SOFTWARE	ARG N:364 , GLU N:375 , BMA N:471C , MAN N:473E , MAN N:474F	BINDING SITE FOR RESIDUE MAN N 472D
5	AC5	SOFTWARE	ARG H:100 , ASP N:330 , ARG N:389 , MAN N:472D , MAN N:474F	BINDING SITE FOR RESIDUE MAN N 473E
6	AC6	SOFTWARE	ARG H:100 , ASP H:100B , ARG N:327 , ASN N:329 , ASP N:330 , ARG N:364 , ILE N:366 , MAN N:472D , MAN N:473E	BINDING SITE FOR RESIDUE MAN N 474F
7	AC7	SOFTWARE	PHE N:84 , ASN N:86 , ASN N:234	BINDING SITE FOR RESIDUE NAG N 475A

SS Bonds (11, 11)

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	L:23	-	L:88
3	N:92	-	N:417
4	N:124	-	N:129
5	N:175	-	N:193
6	N:183	-	N:230
7	N:232	-	N:237
8	N:278	-	N:291
9	N:280	-	N:289
10	N:318	-	N:337
11	N:421	-	N:447

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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 H from PDB  Type:PROTEIN  Length:122
                                                                                                                                                           
               SCOP domains d1nmah_ H: Immunoglobulin heavy chain variable domain, VH                                                                  SCOP domains
               CATH domains 1nmaH00 H:1-113 Immunoglobulins                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeee...eeeeeeeee...hhh.eeeeeeee.....eeeeeee....eeee...hhh.eeeeeehhh.eeeeeee...hhh.eeeeeeee.........eeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                1nma H    1 EVQLQQPGAELVKPGASVRMSCKASGYTFTNYNMYWVKQSPGQGLEWIGIFYPGNGDTSYNQKFKDKATLTADKSSNTAYMQLSSLTSEDSAVYYCARSGGSYRYDGGFDYWGQGTTLTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111  
                                                                              52A                            82A||               100A||||             
                                                                                                              82B|                100B|||             
                                                                                                               82C                 100C||             
                                                                                                                                    100D|             
                                                                                                                                     100E

Chain L from PDB  Type:PROTEIN  Length:109
                                                                                                                                              
               SCOP domains d1nmal_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                         SCOP domains
               CATH domains 1nmaL00 L:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee............eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee....hhh..eeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                1nma L    1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQNPDGTVKLLIYYTSNLHSEVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQDFTLPFTFGGGTKLEIRRA  109
                                    10        20        30        40        50        60        70        80        90       100

Chain N from PDB  Type:PROTEIN  Length:378
 aligned with NRAM_I84A1 | P05803 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:378
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452        
          NRAM_I84A1     83 REFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRDLISWPLSSPPTVYNSRVECIGWSSTSCHDGRARMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCQNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLTGTAKHIEECSCYGEQAGVTCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGGNTWLGRTISIASRSGYEMLKVPNALTDDRSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWNW  460
               SCOP domains d1nman_ N: Influenza neuraminidase                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1nmaN00 N:82-458  [code=2.120.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains Neur-1nmaN01 N:82-458                                                                                                                                                                                                                                                                                                                                                                      Pfam domains
         Sec.struct. author ..............eeeeeeee.hhhhhhh.....eeeeeeeee..eeeeeeee.......hhh...........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeeee.....eeeeeeeee..eeeeeee...........eeee....eeee..........eeeeee....eeeeee...................................eeee..eeeeee.........eeeee.............eeeeee........eeeee..........eeeeeeeeee.........eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1nma N   82 REFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRDLISWPLSSPPTVYNSRVECIGWSSTSCHDGRARMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCQNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLTGTAKHIEECSCYGEQAGVTCTCRDNWQGSNRPVIQIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGGNTWLGRTISIASRSGYEMLKVPNALTDDKSRPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWNW  458
                                    91       101       111       121       131       141       151       161       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  ||   341       351       361       371       381       391||     402       412||     420       430       440       450        
                                                                                                                 169A                                                                                                                                                                 333|                                                      392|               412A|                                              
                                                                                                                                                                                                                                                                                       335                                                       394                412B

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (2, 3)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

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