1o4x: Sequences

PDBeMotif: 1o4x

		Sequences				3D motifs				Ligand environment				Ligand bonds

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Classification:	transcription/dna \| release date: Thu, Jul 17, 2003
Title:	ternary complex of the dna binding domains of the oct1 and sox2 transcription factors with a 19mer oligonucleotide from the hoxb1 regulatory element
Authors:	D.C.WILLIAMS, G.M.CLORE
Method:	SOLUTION NMR

PDBe Citation

Ligand bond colours:

covalent

ionic

hydrogen

electrostatic

van-der-waals

plane-atom

plane-plane

undefined

- Click here to show 5Å bonds

Chain A sequence:
GSHMEEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMAKLKPLLEKWLNDAEN
LSSDSSLSSPSALNSPGIEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK
RINPPSS

Chain B sequence:
GSHMPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPR
RKTKTLMK

Residue colours: hydrophilic hydrophobic intermediate

View the assembly/model: (

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chain:

Sequence numbers:

Using:	φ/ψ residues code secondary structures
	coordinates of: Cαs Side-chain

View the fragment:

chain A : TRANSCRIPTION FACTOR OCT-1 member of: CATH:1.10.10.60/1.10.260.40, GENE3D:G3DSA_1.10.10.60/G3DSA_1.10.260.40, PANTHER:PTHR11636/PTHR11636_SF47, PFAM:PF00046/PF00157, PRINTS:OCTAMER/POUDOMAIN, PROSITE PATTERNS:PS00027/PS00035/PS00465, PROSITE PROFILES:PS50071/PS51179, SMART:SM00352/SM00389, SUPERFAMILY:SSF46689/SSF47413, UniProt:P14859
`sec str:`	`......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...`
`sequence :`	`..EEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMAKLKPLLEKWLNDAE..SIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN`
`seq num:`	`..5 15 25 35 45 55 65 75 ..110 120 130 140 150 160`
`ASN_GLYCOSYLATION`	`..\| \|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \| \|\|\|\| \| \|\|\| \|\|\|\|\|\|\|\|\|\|\|^***\| \|\| \| \|\| \| \| .. \|\|\| \|\| \| \| \|\| \| \| \|\|\| \|\|\| \| \| \|\|\|\|\|\|\|\|\|\|\|`
`CAMP_PHOSPHO_SITE`	`..\| \|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \| \|\|\|\| \| \|\|\| \|\|\|\|\|\|\|\|\|\|\|\| \| \| \|\| \| \|\| \| \| .. \|\|\| \|\| \| \| \|\| \| \| \|\|\| \|\|\| \| \| \|\|\|\|\|\|\|\|\|\|\|`
`PKC_PHOSPHO_SITE`	`..\| \|\|\|\|\|\|\|\|\| ^ \|\|\|\|\|\|\|\| \| \|\|\|\| \| \|\|\| \|\|\|\|\|\|\|\|\|\|\|\| ^ \|\| \| \|\| \| \| .. \|\|\| \|\| \| \| \|\| \| \| \|\|\| \|\|\| \| \| \|\|\|\|\|\|\|\|\|\|\|`
`CK2_PHOSPHO_SITE`	`..* ^*\|\|\|\|\| \|\| \|\|\|\|\|\|\|^* \|\|\|\| \| \|\|\| \|\|\|\|\|^*\|\|\| \| \| \|\| \| \|\| \| \| ..\|\| \|\| ^ ^* \| \|\|\| \|\|\| \| \| \|\|\|\|\|\|\|\|\|\|\|`
`MYRISTYL`	`.. \|\|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\| \| ^*** \|^***\|\|\|\|\|\|\|\|\|\| \| \| \|\| \| \|\| \| \| .. \|\| \|\| \| \| \|\|\| \|\|\| \| \| \|\|\|\|\|\|\|\|\|\|\|`
`HOMEOBOX_1`	`.. \|\|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\| \| \|\|\|\| \| \| \| \|\|\|\|\|\|\|\|\|\| \| \| \|\| \| \|\| \| \| .. \|\| \|\| \| \| ************************\|`
`POU_1`	`.. \|\|\|\|\|\|\|\| \|\| *************\|\|\| \| \| \| \|\|\|\|\|\|\|\|\|\| \| \| \|\| \| \|\| \| \| .. \|\| \|\| \| \| \|\| \|\|\| \| \| \|\|\|\|\|\|\|\|\|\|\|`
`POU_2`	`.. \|\|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\| \| \|\|\|\| \| \| ************** \| \|\| \| \|\| \| \| .. \|\| \|\| \| \| \|\| \|\|\| \| \| \|\|\|\|\|\|\|\|\|\|\|`
`alphabetamotif`	`.. *****\| ****\|\| *\| \| \| ***\|\|\| * * \| \| .. \|\| \|\| \| \| \|\| \|\|\| \| \| ********\|`
`asxmotif`	`.. *****\| \| \|\| \|\|\|\|\|\|\| \| \|\| \| \| \| \|\|\|\|\|\| \|\|\| \| \| \| \| \| \| .. \|\| \|\| \| \| \|\| \|\|\| \| \| \|\|\|\|\|\| \|\| \|`
`betaturn`	`.. ****** *****\| ** \| \| *****\| .. * \| ****\| ******* \|`
`nest`	`.. * * \| * .. \| \| * \| \|`
`niche`	`.. \| \| .. \| \| ****`
`schellmannloop`	`.. ****** .. \| \|`
`ststaple`	`.. .. *****`

chain B : TRANSCRIPTION FACTOR SOX-2 member of: CATH:1.10.30.10, GENE3D:G3DSA_1.10.30.10, PANTHER:PTHR10270/PTHR10270_SF47, PFAM:PF00505/PF12336, PROSITE PROFILES:PS50118, SMART:SM00398, SUPERFAMILY:SSF47095, UniProt:P48431
`sec str:`	`.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........`
`sequence :`	`..DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRK`
`seq num:`	`..206 216 226 236 246 256 266 276`
`CAMP_PHOSPHO_SITE`	`.. \|\| \|\| \| \|\|\|\|\|\| \| \| \| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\| \| \|\|\|\|\|\|\|\|\| \| \| **^`
`PKC_PHOSPHO_SITE`	`.. \|\| \|\| \| \|\|\|\|\|\| \| \| ^\|\|\|\|\|\|\|\|\|\|^\| \|\| \| \|\|\|\|\|\|\|\|\| \| \|`
`CK2_PHOSPHO_SITE`	`.. \|\| \|\| \| \|\|\|\|\|\| \| \| \| \|\|\|\|\|\|\|\|^***\|\| \|\| \| \|\|\|\|\|\|\|\|\| \| \|`
`TYR_PHOSPHO_SITE`	`.. \|\| \|\| \| \|\|\|\|\|\| \| \| \| \|\|\|\|\|\|\|\| \|\| \|\| \|\| \| \|\|\|\|\|\|*******^`
`alphabetamotif`	`.. \|\| \|\| *****\| \| \| \| \|\|\|\|\|\|\|\| \|\| * *********\| \|`
`betaturn`	`.. *** **** \| \| \| ***\| *** ******** \| \|`
`niche`	`.. ** \| \| **`
`ststaple`	`.. *****`

*chain C : 5'-D(TPGPTPCPTPTPTPGPTPCPAPTPGPCPTPAPAPTPG)-3';**
`sec str:`	`.....................`
`sequence :`	`..TGTCTTTGTCATGCTAATG`
`seq num:`	`..301 311`

*chain D : 5'-D(CPAPTPTPAPGPCPAPTPGPAPCPAPAPAPGPAPCPA)-3';**
`sec str:`	`.....................`
`sequence :`	`..CATTAGCATGACAAAGACA`
`seq num:`	`..320 330`

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