Database Description

Protein Biological Unit Database
(ProtBuD)

About

SCOP: Domain information from SCOP ScopDomain: SCOP domain classification information in the hierarchy ScopDomainPos: SCOP domain residue range ScopDescription: SCOP hierarchy level description PDB PdbEntry: PDB entry data PdbBuGen: Symmetry operators to generate PDB BU EntryKeywords: Keywords for PDB entry BiolUnit: RCSB biological units AsymUnit: Asymmetric chains PdbModRes: Modified resiude PdbCovale: Covalent chains PQS PqsPdbChainMap: PQS chain and author chain map PqsBuStat: Summary data for PQS macro molecule PDB Hit PsiBlastHit: Homologous hits RedundantPdbChains: Redundant chains in PDB PDB/PQS BU Comparison PdbPqsBuComp: PDB/PQS entry biological units comparison PdbPqsBuInterfaces: Interface pairs and scores
Category	Table Names	Columns	Description	Example
SCOP	ScopDomain	SunID	Unique number for SCOP domain	42538
		PdbID	4-character PDB code	1d1w
		OldScopID	SCOP code replaced by SunID	d1d1wa_
		Class	SCOP class	d
		Fold	SCOP fold	174
		Superfamily	SCOP superfamily	1
		Family	SCOP family	1
		Protein	SCOP protein number in the family based on the hierarchical tree node order	1
		Species	SCOP species number in the protein based on the hierarchical tree node order	4

	ScopDomainPos	SunID	Unique number for SCOP domain	42538
		Chain	Author chain ID	A
		StartPos	start residue number of domain	- (whole chain)
		EndPos	end residue number of domain	- (whole chain)

	ScopDescription	Class	SCOP class	d
		Fold	SCOP fold	174
		Superfamily	SCOP superfamily	1
		Family	SCOP family	1
		Protein	SCOP protein number in the family based on the hierarchical tree node order	-
		Species	SCOP species number in the protein based on the hierarchical tree node order	-
		Description	name of the level	Nitric oxide (NO) synthase oxygenase domain

PDB	PdbEntry	PdbID	4-characters PDB code	1d1w
		NumOfLigandAtoms	Number of ligand atoms	179
		Method	Experimental method	X-ray diffraction
		Resolution	Resolution	2.0
		R_Factor	Work R factor	0.204
		Free R_Factor	Free R factor	0.25
		Length_a	Length in dimension a in cryst1	58.46
		Length_b	Length in dimension b in cryst1	106.32
		Length_c	Length in dimension c in cryst1	156.33
		Angle_Alpha	Alpha angle in cryst1	90
		Angle_Beta	Beta angle in cryst1	90
		Angle_Gamma	Gamma angle in cryst1	90
		Z_PDB	The number of molecules in cryst1	8
		SpaceGroup	Space group in cryst1	P 21 21 2

	PdbBuGen	PdbID	4-characters PDB code	1d1w
		AsymID	Asymmetric chain ID	A
		BiolUnitID	Biological unit ID	1
		SymOpNum	Symmetry operation number	1
		SymString	Symmetry operation string	555
		FullSymString	Full symmetry operation string	X,Y,Z

	EntryKeywords	PdbID	4-characters PDB code	1d1w
	EntryKeywords	Keyword	keywords	Oxidoreductase

	BiolUnit	PdbID	4-characters PDB code	1d1w
		AsymID	Asymmetric chain ID	A
		BiolUnitID	Biological unit ID	1
		NumOfMols	Number of asymmetric chain copies	1

	AsymUnit	PdbID	4-characters PDB code	1d1w
		AsymID	Asymmetric chain ID	A
		AuthorChainID	Author named chain ID	A
		EntityID	Entity number	1
		IsModified	Asymmetric chain is modified or not	N
		PolymerStatus	Entity is a polymer or not	polymer
		PolymerType	Polymer Type	polypeptide(L)
		NameSource	The source of name (SwissProt, RCSB and PDB)	sws
		Name	Entity name	Nitric-oxide synthase, endothelial
		Sequence	Residue sequence	skip (sequence too long)
		SequenceInCoord	Residue sequence with coordinate	skip (sequence too long)

	PdbModRes	PdbID	4-characters PDB code	9wga
		ModResID	Unique code of modified residues	ModRes1
		AsymID	Asymmetric chain ID	A
		ModRes	Modified residue	PCA
		StdRes	Standard residue	GLU
		SeqID	Residue sequence number	1
		AuthorChain	Author named chain ID	A
		AuthorRes	Author named residue name	PCA
		AuthorSeqID	Author named residue sequence number	1
		Details	Description of modification	Pyroglutamic acid

	PdbCovale	PdbID	4-characters PDB code	9rub
		CovaleID	Unique code of covalent	covale1
		CovaleAsymID	Covalent asymmetric chain ID	A
		CovaleCompID	Covalent compound name	LYS
		CovaleSeqID	Covalent sequence ID	191
		CovaleAtomID	Covalent atom ID	NZ
		AttachAsymID	Attached asymmetric chain ID	G
		AttachCompID	Attached compound name	CBX
		AttachSeqID	Sequence ID in the attached chain	-
		AttachAtomID	Atom ID in the attached chain	C
		AuthorCovaleAsymID	Covalent author chain ID	A
AuthorCovaleCompID		Covalent author compound name	CBX
AuthorCovaleSeqID		Author sequence ID of covalent	191
AuthorAttachAsymID		Attached author chain ID	A
AuthorAttachCompID		Attached compound name	CBX
AuthorAttachSeqID		Author sequence ID of attached residue	191

PQS	PqsPdbChainMap	PdbID	4-characters PDB code	1d1w
		PqsBiolUnitID	Biological unit ID from PQS	1
		PqsChainID	PQS chain ID	C
		PdbChainID	The corresponding author chain in PDB	_
		PdbChainID	The corresponding author chain in PDB	_
		SymOpNum	The symmetry operator number in the space group	1
		FullSymString	The full symmetry string	X,Y,Z

	PqsBuStat	PdbID	4-characters PDB code	1d1w
		PqsBiolUnitID	Biological unit ID	1
		IsXPack	The macro molecule is cystal packing	0
		BiolClass	Is this homo multimer	1
		BiolType	Multimer type	Dimer
		NumChains	Number of chains in the macro molecule	2
		NumResid	Number of residues in the macro molecule	830
		NumHBonds	Number of hydro bonds in the macro molecule	179
		DeltaAsa	Difference of ASA	3080
		DeltaSole	Difference of solvent ASA	-36.03
		NumSs	The number of sulfate bridge	0
		NumSaltbridge	The number of salt bridge	1
		NumBuried	The number of buried	0
		BiolScore	The score for biological unit	0.595
		IsHighRms	Is it high RMS	0
		BiolForm	Chain format of the biological unit	[A2]

PDB Hit	RedundantPdbChains	PdbID1	Representative PDB code	1d0c
		ChainID1	Representative PDB author chain ID	A
		PdbID2	Redundant PDB code	1d1w
		ChainID2	Redundant PDB author chain	A

	PsiBlastHit	QueryEntry	Query PDB code	1d0c
		QueryChain	Query author chain ID	A
		HitEntry	Hit PDB code return by PSI BLAST	1dd7
		HitChain	Hit author chain ID	A
		QueryLength	Total residue number of query sequence	444
		HitLength	Total residue number of hit sequence	389
		Identity	Identity percentage between query and hit	63
		AlignmentLength	Alignment length	377
		E_value	E value	0
		QueryStart	Alignment start residue number of query	68
		QueryEnd	Alignment end residue number of query	444
		HitStart	Alignment start residue number of Hit	1
		HitEnd	Alignment end residue number of Hit	37

PDB/PQS BU Comp	PdbPqsBuComp	PdbID	4-characters of PDB code	1d1w
		PdbBuID	PDB biological unit ID	1
		PqsBuID	PQS biological unit ID	1
		PdbInterfaceNum	The number of interfaces in PDB biological unit	1
		PqsInterfaceNum	The number of interfaces in PQS biological unit	1
		IsSame	Are two biological units same	1

	PdbPqsBuInterfaces	PdbID	4-characters of PDB code	1d1w
		PdbBuID	PDB biological unit ID	1
		PqsBuID	PQS biological unit ID	1
		PdbBuChain1	Asymmetric chain with symmetry operator in the interface	A_1_555
		PdbBuChain2	Asymmetric chain with symmetry operator in the interface	B_1_555
		PqsBuChain1	PQS chain in the interface	A
		PqsBuChain2	PQS chain in the interface	B
		QScore	Q score	1.0