SMTL ID : 4d90.3 (2 other biounits)

Crystal Structure of Del-1 EGF domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Post Translational Modification)

NGA.1: 1 residues within 4Å: Chain A: T.50 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.50 NGA.5: 2 residues within 4Å: Chain B: T.50, A.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.52

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain A: N.117, Y.118, R.129 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.117

2 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.3: 5 residues within 4Å: Chain A: G.63, T.65, K.83, C.84, P.85 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.63 FUC.7: 5 residues within 4Å: Chain B: G.63, T.65, K.83, C.84, P.85 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: N.96, I.97, E.99, D.113, L.114 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.97, A:E.99, A:D.113, A:L.114, H2O.1 CA.8: 5 residues within 4Å: Chain B: N.96, I.97, E.99, D.113, L.114 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.97, B:E.99, B:D.113, B:L.114, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schurpf, T. et al., The RGD finger of Del-1 is a unique structural feature critical for integrin binding. Faseb J. (2012)

Release Date

2012-05-30

Peptides

EGF-like repeat and discoidin I-like domain-containing protein 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EGF-like repeat and discoidin I-like domain-containing protein 3

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