OLIGAMI : Oligomer Architecture and Molecular Interface

Title

CRYSTAL STRUCTURE OF LIGD IN COMPLEX WITH NADH FROM SPHINGOBIUM SP. STRAIN SYK-6

Structure Summary

PDB ID	Mutant	OPM	Pub Med	Method/Resolution	HETNAM
4y9d			26940872	X-RAY DIFFRACTION/2.01	NAI:1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Chain Formula
Amino Acid sequence	SCOPe Family Level	CATH Homology Level
[A2]	[A2]	[A2]

Interfaces

Interface ID	Chain	Inaterface Class	Interface Type	Contact Type
4y9d_AB	A B	HN HN	i9_CR(H35,N17)_HH(P1,A1,S3)_HN(L3,S6) i9_CR(H35,N17)_HH(P1,A1,S3)_HN(L3,S6)	c2_RP(HH58,NN22,HN30,NH24)_HH(P1,A4,S4)_HN(L6,S6) c2_RP(HH58,NN22,HN30,NH24)_HH(P1,A4,S4)_HN(L6,S6)

Interface Class

Interface ID	Interface 1						Interface 2
	Domain	Number of contact residues	Binding site Class	Percentages of Secondary structures(%)			Domain	Number of contact residues	Binding site Class	Percentages of Secondary structures(%)
	Domain	Number of contact residues	Binding site Class	H	E	N	Domain	Number of contact residues	Binding site Class	H	E	N
4y9d_AB	A	58	HN	58.6	100	39.7	B	58	HN	58.6	1.7	39.7

Interface Type: Information for each interface

Interface ID	chain	Number of contact residues			Number of elements					Number of contacts between Secondary structure elements
		Number of contact residues			Number of elements					HH			EE						HE			HN		EN
		Hn	En	Nn	H	E	N	R	L	P	A	S	P	A	S	Ph	Ah	Ih	P	A	S	L	S	L	S
4y9d_AB	A	34	58	23	5	1	6	0	0	1	0	1	0	0	0	0	0	0	0	0	1	4	7	0	1
4y9d_AB	B	34	1	23	5	1	6	0	0	1	0	1	0	0	0	0	0	0	0	0	1	4	7	0	1

Contact Type: Information of contacts between interfaces

Interface ID	Number of residue pairs between SS elements									Number of contacts between Secondary structure elements
	H-H	E-E	N-N	H-E	H-N	N-E	E-H	N-H	E-N	H-H				E-E					H-E				H-N			E-N
	H-H	E-E	N-N	H-E	H-N	N-E	E-H	N-H	E-N	P	A	S	Ih	P	A	S	IPh	IAh	P	A	S	Ih	L	S	Ih	L	S	Ih
4y9d_AB	53	0	27	4	30	0	4	30	0	0	4	6	0	0	0	0	0	0	0	2	0	0	4	8	2	0	0	0

Structual Classification

SCOPe

SCOPe ID	Chain	Class	Fold	Superfamily	Family	Protein Domain	Species
311973	A:	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	Sphingobium sp. [TaxId: 627192]

CATH

CATH ID	Node	Class	Architecture	Topology	Homology
4y9dA00	3.40.50.720		:3-Layer(aba) Sandwich	:Rossmann fold	:NAD(P)-binding Rossmann-like Domain