4GVD: T-cell Lymphoma Invasion and Metastasis-1 PDZ

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with Syndecan1 Peptide. Determined by X-ray diffraction at 1.85 Å resolution. Released 13 Mar 2013.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,566
Mol. weight: 23 kDa
Ligands: ANS
Released: 13 Mar 2013

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

Secondary structure: helices and β-sheets

4GVD contains 7 α-helices and 14 β-strands across 4 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: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	843-849	7	1
β-strand	860-865	6	1
β-strand	872-878	7	1
α-helix	883-886	4
α-helix	893	1
β-strand	894-898	5	1
β-strand	901-902	2	1
α-helix	908-916	9
β-strand	919-925	7	1

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	842-849	8	1
β-strand	860-867	8	1
β-strand	870-878	9	1
α-helix	883-886	4
α-helix	893	1
β-strand	894-898	5	1
β-strand	901-902	2	1
α-helix	903-905	3
α-helix	908-915	8
β-strand	919-926	8	1

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-7	5	1

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-7	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-lymphoma invasion and metastasis-inducing protein 1	A, B	protein	94	Homo sapiens	Q13009 (AlphaFold model)
Syndecan-1	C, D	protein	8	Homo sapiens	P18827 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4GVD_1 T-lymphoma invasion and metastasis-inducing protein 1 (chains A, B)
GAMGKVTHSIHIEKSDTAADTYGFSLSSVEEDGIRRLYVNSVKETGLASKKGLKAGDEIL
EINNRAADALNSSMLKDFLSQPSLGLLVRTYPEL

Sequence of entity 2 (C, D), FASTA

>4GVD_2 Syndecan-1 (chains C, D)
TKQEEFYA

Ligands and cofactors

ID	Name	Formula	Copies
ANS	5-(dimethylamino)-1-naphthalenesulfonic acid(dansyl acid)	C12 H13 N O3 S	2

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. Liu, X., Shepherd, T.R., Murray, A.M. et al. Structure (2013) 21:342-354. DOI 10.1016/j.str.2013.01.004 · PubMed

Other PDB entries of the same protein (UniProt Q13009 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KZD 1.3 Å, Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain
4GVC 1.54 Å, Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with…
3KZE 1.8 Å, Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in Complex With…
4NXR 1.9 Å, Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple…
4K2P 1.98 Å, The Structure of a Quintuple Mutant of the Tiam1 PH-CC-Ex Domain
4NXQ 2.1 Å, Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple…
4K2O 2.15 Å, The Structure of a Triple Mutant of the Tiam1 PH-CC-Ex Domain
4NXP 2.3 Å, Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple…
2D8I Solution structure of the PDZ domain of T-cell lymphoma invasion and metastasis 1 varian

Browse structure collections

About this viewer

MolViewer shows 4GVD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.