4GEJ: N-terminal domain of VDUP-1

N-terminal domain of VDUP-1. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Feb 2013.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,938
Mol. weight: 171.27 kDa
Ligands: CA
Released: 27 Feb 2013

Explore 4GEJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GEJ contains 21 α-helices and 126 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	1
β-strand	21	1	2
β-strand	26-34	9	1
β-strand	35	1	3
β-strand	39-41	3	4
β-strand	43-53	11	5
β-strand	55-58	4	6
β-strand	60-65	6	6
β-strand	67-75	9	5
β-strand	89-91	3	4
β-strand	93	1	3
β-strand	97-104	8	1
α-helix	105-106	2
β-strand	120-131	12	5
β-strand	134-142	9	5
β-strand	145	1	2

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	7
β-strand	20-21	2	8
α-helix	25	1
β-strand	26-34	9	7
β-strand	39-41	3	9
β-strand	43-58	16	6
β-strand	61-76	16	6
β-strand	89-91	3	9
β-strand	97-104	8	7
β-strand	120-130	11	6
α-helix	135-136	2
β-strand	137-142	6	6
β-strand	144-145	2	8

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	10
β-strand	21	1	11
β-strand	26-34	9	10
β-strand	39-41	3	12
β-strand	43-58	16	6
β-strand	60-76	17	6
β-strand	89-91	3	12
β-strand	97-104	8	10
α-helix	105-106	2
β-strand	115	1	13
β-strand	117	1	13
β-strand	120-130	11	6
α-helix	135-136	2
β-strand	137-142	6	6
β-strand	145	1	11

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	14
β-strand	20-22	3	15
α-helix	25	1
β-strand	26-34	9	14
β-strand	39-41	3	16
β-strand	43-57	15	6
β-strand	62-76	15	6
β-strand	89-91	3	16
β-strand	97-104	8	14
α-helix	105-106	2
β-strand	121-130	10	6
β-strand	137-142	6	6
β-strand	144-146	3	15

Chain E: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	17
β-strand	21	1	18
β-strand	26-34	9	17
β-strand	39-41	3	19
β-strand	43-57	15	6
β-strand	62-76	15	6
α-helix	88	1
β-strand	89-91	3	19
β-strand	97-104	8	17
α-helix	105-106	2
β-strand	114	1	20
β-strand	116	1	20
β-strand	121-130	10	6
α-helix	135-136	2
β-strand	137-142	6	6
β-strand	145	1	18

Chain F: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	21
β-strand	21-22	2	22
β-strand	26-34	9	21
β-strand	39-41	3	23
β-strand	43-53	11	24
β-strand	55-58	4	6
β-strand	61-64	4	6
β-strand	67-76	10	24
β-strand	89-91	3	23
β-strand	97-104	8	21
β-strand	120-130	11	24
α-helix	135-136	2
β-strand	137-142	6	24
β-strand	145-146	2	22

Chain G: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	25
β-strand	21-22	2	26
β-strand	26-34	9	25
β-strand	39-41	3	27
β-strand	43-53	11	28
β-strand	56	1	6
β-strand	57	1	29
β-strand	61-64	4	29
β-strand	66-76	11	28
β-strand	89-91	3	27
β-strand	97-104	8	25
α-helix	105-106	2
β-strand	122-130	9	28
α-helix	135-136	2
β-strand	137-142	6	28
β-strand	145-146	2	26

Chain H: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	30
α-helix	19-20	2
β-strand	21-22	2	31
β-strand	26-34	9	30
β-strand	39-41	3	32
β-strand	43-54	12	33
β-strand	55-57	3	29
β-strand	62-65	4	29
β-strand	67-76	10	33
β-strand	89-91	3	32
β-strand	97-104	8	30
α-helix	105-106	2
β-strand	119-130	12	33
α-helix	135-136	2
β-strand	137-142	6	33
β-strand	145-146	2	31

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thioredoxin-interacting protein	A, B, C, D, E, F, G, H, I, J	protein	150	Homo sapiens	Q9H3M7 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>4GEJ_1 Thioredoxin-interacting protein (chains A, B, C, D, E, F, G, H, I, J)
SNVMFKKIKSFEVVFNDPEKVYGSGERVAGRVIVEVSEVTRVKAVRILASGVAKVLWMQG
SQQCKQTSEYLRYEDTLLLEDQPTGENEMVIMRPGNKYEYKFGFELPQGPLGTSFKGKYG
SVDYWVKAFLDRPSQPTQETKKNFEVVDLV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	5

Primary citation

Structure of the N-terminal domain of human thioredoxin-interacting protein. Polekhina, G., Ascher, D.B., Kok, S.F. et al. Acta Crystallogr D Biol Crystallogr (2013) 69:333-344. DOI 10.1107/S0907444912047099 · PubMed

Other PDB entries of the same protein (UniProt Q9H3M7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CQ2 1.4 Å, Crystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide
4GEI 1.5 Å, N-terminal domain of VDUP-1
5DZD 1.57 Å, Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide
4GFX 1.6 Å, Crystal structure of the N-terminal domain of TXNIP
5DWS 1.65 Å, Crystal Structure of ITCH WW3 domain in complex with TXNIP peptide
5DF6 1.78 Å, Crystal structure of PTPN11 tandem SH2 domains in complex with a TXNIP peptide
4ROJ 1.95 Å, Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide
4LL1 2.0 Å, The structure of the TRX and TXNIP complex
4ROF 2.03 Å, Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide
4LL4 2.7 Å, The structure of the TRX and TXNIP complex

Browse structure collections

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