CATH Domain: 2iojA00

2iojA00

PDB 2ioj, Chain A, Domain 0

CATH Code	Level Description	Links
3	Alpha Beta
3.40	3-Layer(aba) Sandwich
3.40.1390	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
3.40.1390.20		Gene3D
3.40.1390.20.2
3.40.1390.20.2.1
3.40.1390.20.2.1.1
3.40.1390.20.2.1.1.1
3.40.1390.20.2.1.1.1.1

Structure
Sequence
History

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Segment boundaries for domain 2iojA00

Domain	Start PDB Residue	Stop PDB Residue
2iojA00	206	325

What is a Structural Neighbour?

The term "structural neighbour" is used here to describe two CATH domains that share a degree of structural similarity. The SSAP algorithm is used to calculate this similarity and works by generating a structure-based pairwise alignment of the two domains then scoring this alignment using a RMSD score which has been normalised by the length of the larger domain divided by the number of aligned residues (SIMAX).

Structural Neighbourhood (2 entries)

There are 2 matching structural neighberhood comparisons for CATH ID 3.40.1390.20.2.1.1.1.1 (SIMAX score < 5)

Match Depth	Match	SSAP score	Match Keywords	Match Superfamily	Length	Sequence Id	Overlap	RMSD	SIMAX
	1nmpA01	78.61	UPF0135 protein ybgIEscherichia coli K-12	3.40.1390.30	119	7	79	3.58	4.48
	1knxA01	77.65	HPr kinase/phosphorylaseMycoplasma pneumoniaeHPr kinase/phosphorylase [EC:2.7.11.- 2.7.4.-]	3.40.1390.20	133	14	86	3.89	4.50

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Domain ATOM Sequence

>pdb|2iojA00
GLSVEEIREAVSGEYLIEPREEKVEQVVIGASPQSALRYLREARNAALVTGGDRSDLLLTALEPNVRCLILTGNLEPVQL
VLTKAEERGVPVILTGHDTLTAVSRLESVFGRTRIRG

BLAST against CATH

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Domain COMBS Sequence

>pdb|2iojA00
RNPVLAGLSVEEIREAVSGEYLIEPREEKXVEQVVIGAXSPQSALRYLREARNAALVTGGDRSDLLLTALEXPNVRCLIL
TGNLEPVQLVLTKAEERGVPVILTGHDTLTAVSRLESVFGRTRIRGEPKVGIXRELFES

BLAST against CATH

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Domain History Events (12)

Domain assigned by auto on 12 Feb 2008 20:16

Assigning to "3.40.1390.20" based on similarity with "2iojB00"