SMTL ID : 3d34.1

Structure of the F-spondin domain of mindin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 2 residues within 4Å: Chain A: E.73, N.175 No protein-ligand interaction detected (PLIP) NI.2: 5 residues within 4Å: Chain A: E.96 Ligands: NI.3, NI.4, NI.6, NI.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.96, H2O.11 NI.3: 4 residues within 4Å: Chain A: K.16 Ligands: NI.2, NI.6, NI.7 No protein-ligand interaction detected (PLIP) NI.4: 4 residues within 4Å: Chain A: E.96, E.115 Ligands: NI.2, NI.6 No protein-ligand interaction detected (PLIP) NI.6: 5 residues within 4Å: Chain B: K.16 Ligands: NI.2, NI.3, NI.4, NI.7 No protein-ligand interaction detected (PLIP) NI.7: 5 residues within 4Å: Chain B: K.16, E.96 Ligands: NI.2, NI.3, NI.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.96, H2O.11

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: D.134, D.162, D.166 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.134, A:D.162, H2O.1, H2O.4, H2O.4 CA.8: 3 residues within 4Å: Chain B: D.134, D.162, D.166 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.134, B:D.134, B:D.162, H2O.7, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule. Embo J. (2009)

Release Date

2009-02-17

Peptides

Spondin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spondin-2