4F8L - JenaLib

Title :   X-RAY STRUCTURE OF PSAA FROM YERSINIA PESTIS, IN COMPLEX WITH GALACTOSE AND AEBSF

Authors :   R. Bao, L. Esser, D. Xia

Date :   17 May 12 (Deposition) - 22 May 13 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Antigens, Bacterial Proteins, Fimbriae, Molecular Sequence Data, Protein Folding, All Beta-Strand, Ig-Fold, Adhesion, Cell Adhesion- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Bao, M. K. Nair, W. K. Tang, L. Esser, A. Sadhukhan, R. L. Holland, D. Xia, D. M. Schifferli
Structural Basis For The Specific Recognition Of Dual Receptors By The Homopolymeric Ph 6 Antigen (Psa) Fimbriae Of Yersinia Pestis.
Proc. Natl. Acad. Sci. Usa V. 110 1065 2013
PubMed-ID: 23277582 | Reference-DOI: 10.1073/PNAS.1212431110

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 41)

Sites (40, 40)

Asymmetric Unit (40, 40)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:41 , ASP A:74 , ASN A:76 , ASN A:80 , TYR A:113 , BR A:221 , HOH A:332	BINDING SITE FOR RESIDUE GAL A 201
02	AC2	SOFTWARE	HIS A:90	BINDING SITE FOR RESIDUE BR A 202
03	AC3	SOFTWARE	TYR A:60 , BR A:222	BINDING SITE FOR RESIDUE BR A 203
04	AC4	SOFTWARE	GLY A:72 , ILE A:73 , HOH A:333 , HOH A:419	BINDING SITE FOR RESIDUE BR A 204
05	AC5	SOFTWARE	ASP A:7 , THR A:28 , THR A:30	BINDING SITE FOR RESIDUE BR A 205
06	AC6	SOFTWARE	LYS A:85 , ASP A:86	BINDING SITE FOR RESIDUE BR A 206
07	AC7	SOFTWARE	LYS A:88 , HOH A:331	BINDING SITE FOR RESIDUE BR A 207
08	AC8	SOFTWARE	GLN A:136	BINDING SITE FOR RESIDUE BR A 208
09	AC9	SOFTWARE	VAL A:122	BINDING SITE FOR RESIDUE BR A 209
10	BC1	SOFTWARE	SER A:125	BINDING SITE FOR RESIDUE BR A 210
11	BC2	SOFTWARE	VAL A:6 , LYS A:126	BINDING SITE FOR RESIDUE BR A 211
12	BC3	SOFTWARE	GLY A:130 , GLU A:131	BINDING SITE FOR RESIDUE BR A 212
13	BC4	SOFTWARE	ASN A:75	BINDING SITE FOR RESIDUE BR A 213
14	BC5	SOFTWARE	TRP A:70	BINDING SITE FOR RESIDUE BR A 214
15	BC6	SOFTWARE	GLY A:38 , PHE A:115 , ASN A:117	BINDING SITE FOR RESIDUE BR A 215
16	BC7	SOFTWARE	LYS A:118	BINDING SITE FOR RESIDUE BR A 216
17	BC8	SOFTWARE	THR A:34 , HOH A:442	BINDING SITE FOR RESIDUE BR A 217
18	BC9	SOFTWARE	PHE A:8 , LYS A:126 , BR A:227	BINDING SITE FOR RESIDUE BR A 218
19	CC1	SOFTWARE	HIS A:5 , ASP A:7 , HOH A:358	BINDING SITE FOR RESIDUE BR A 219
20	CC2	SOFTWARE	LYS A:135	BINDING SITE FOR RESIDUE BR A 220
21	CC3	SOFTWARE	SER A:120 , GAL A:201 , BR A:226 , HOH A:311	BINDING SITE FOR RESIDUE BR A 221
22	CC4	SOFTWARE	THR A:45 , GLY A:46 , BR A:203 , HOH A:321	BINDING SITE FOR RESIDUE BR A 222
23	CC5	SOFTWARE	ASP A:127 , HOH A:310 , HOH A:423	BINDING SITE FOR RESIDUE BR A 223
24	CC6	SOFTWARE	HOH A:329	BINDING SITE FOR RESIDUE BR A 224
25	CC7	SOFTWARE	ASP A:57 , LYS A:100 , BR A:231	BINDING SITE FOR RESIDUE BR A 225
26	CC8	SOFTWARE	GLN A:119 , SER A:120 , BR A:221	BINDING SITE FOR RESIDUE BR A 226
27	CC9	SOFTWARE	VAL A:128 , SER A:129 , BR A:218 , HOH A:325 , HOH A:418 , HOH A:426	BINDING SITE FOR RESIDUE BR A 227
28	DC1	SOFTWARE	THR A:45 , TYR A:78 , ASN A:80 , BR A:233 , HOH A:337	BINDING SITE FOR RESIDUE BR A 228
29	DC2	SOFTWARE	VAL A:98 , MLI A:241	BINDING SITE FOR RESIDUE BR A 229
30	DC3	SOFTWARE	ASP A:57 , LYS A:94 , BR A:225	BINDING SITE FOR RESIDUE BR A 231
31	DC4	SOFTWARE	LYS A:88 , HIS A:90 , HOH A:434	BINDING SITE FOR RESIDUE BR A 232
32	DC5	SOFTWARE	THR A:45 , GLY A:108 , ASP A:127 , BR A:228 , HOH A:337 , HOH A:351	BINDING SITE FOR RESIDUE BR A 233
33	DC6	SOFTWARE	BR A:236 , HOH A:367	BINDING SITE FOR RESIDUE BR A 234
34	DC7	SOFTWARE	ASP A:47 , LYS A:49 , TYR A:52 , TYR A:60	BINDING SITE FOR RESIDUE GAI A 235
35	DC8	SOFTWARE	GLY A:137 , BR A:234	BINDING SITE FOR RESIDUE BR A 236
36	DC9	SOFTWARE	HOH A:348 , HOH A:430	BINDING SITE FOR RESIDUE BR A 237
37	EC1	SOFTWARE	SER A:65 , TRP A:77 , LYS A:105 , AES A:239 , GLY A:240	BINDING SITE FOR RESIDUE BR A 238
38	EC2	SOFTWARE	GLY A:50 , GLY A:51 , TYR A:52 , LEU A:63 , TYR A:64 , TRP A:70 , GLY A:72 , ASN A:75 , BR A:238 , GLY A:240 , MLI A:241 , HOH A:396 , HOH A:440	BINDING SITE FOR RESIDUE AES A 239
39	EC3	SOFTWARE	TYR A:64 , TRP A:70 , ILE A:73 , BR A:238 , AES A:239 , HOH A:305 , HOH A:340 , HOH A:371 , HOH A:440	BINDING SITE FOR RESIDUE GLY A 240
40	EC4	SOFTWARE	LYS A:49 , TYR A:60 , GLY A:62 , THR A:97 , BR A:229 , AES A:239	BINDING SITE FOR RESIDUE MLI A 241

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......ee....eeeeeeeee......eeeeee.hhhh..eeee....eee.ee...eeehhhheeeee......eeeeeee....ee...eeeeeeeeeeeeee..eeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8l A   2 NTFHVDFAPNTGEIFAGKQPGDVTMFTLTMGDTAPHGGWRLIPTGDSKGGYMISADGDYVGLYSYMMSWVGIDNNWYINDDSPKDIKDHLYVKAGTVLKPTTYKFTGRVEEYVFDNKQSTVINSKDVSGEVTVKQGLEG 240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       ||
                                                                                                                                                                   139|
                                                                                                                                                                    240

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

Visualization

Interactive Views

Asymmetric/Biological 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
		AES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MLI	[ 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 ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]
		DC1	[ RasMol ]	+environment [ RasMol ]
		DC2	[ RasMol ]	+environment [ RasMol ]
		DC3	[ RasMol ]	+environment [ RasMol ]
		DC4	[ RasMol ]	+environment [ RasMol ]
		DC5	[ RasMol ]	+environment [ RasMol ]
		DC6	[ RasMol ]	+environment [ RasMol ]
		DC7	[ RasMol ]	+environment [ RasMol ]
		DC8	[ RasMol ]	+environment [ RasMol ]
		DC9	[ RasMol ]	+environment [ RasMol ]
		EC1	[ RasMol ]	+environment [ RasMol ]
		EC2	[ RasMol ]	+environment [ RasMol ]
		EC3	[ RasMol ]	+environment [ RasMol ]
		EC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4f8l)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4f8l
		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
	PSAA_YERPE \| P31522
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		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

Description