SMTL ID : 3q13.2 (1 other biounit)

The Structure of the Ca2+-binding, Glycosylated F-spondin Domain of F-spondin, A C2-domain Variant from Extracellular Matrix

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: Y.28, N.30, L.111, R.218 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain B: Y.28, N.30, L.111, R.218 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.141, D.170, D.174 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.141, A:D.141, A:D.170, H2O.10, H2O.10 CA.8: 3 residues within 4Å: Chain B: D.141, D.170, D.174 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.141, B:D.141, B:D.170, H2O.23, H2O.23

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: I.12, L.13, D.14, C.15, K.57, R.125, H.128 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.14, A:C.15 Water bridges: A:K.57, A:T.126 Salt bridges: A:K.57, A:R.125, A:H.128 SO4.4: 6 residues within 4Å: Chain A: R.43 Chain B: Y.40, P.41, R.42, R.43, E.180 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.42, B:R.43 Water bridges: B:D.39, B:Y.40, B:A.44 Salt bridges: A:R.43 SO4.5: 5 residues within 4Å: Chain A: R.42, R.43 Chain B: R.42, R.43 Ligands: SO4.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.42, B:R.43, A:R.42, A:R.43 SO4.9: 7 residues within 4Å: Chain B: I.12, L.13, D.14, C.15, K.57, R.125, H.128 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.14, B:C.15 Water bridges: B:K.57, B:T.126 Salt bridges: B:K.57, B:R.125, B:H.128 SO4.10: 6 residues within 4Å: Chain A: Y.40, P.41, R.42, R.43, E.180 Chain B: R.43 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:R.43 Hydrogen bonds: A:R.42, A:R.43 Water bridges: A:D.39, A:Y.40, A:A.44 SO4.11: 5 residues within 4Å: Chain A: R.42, R.43 Chain B: R.42, R.43 Ligands: SO4.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.42, B:R.43, A:R.42, A:R.43

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: R.89, L.96, T.97, V.98 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.97 Water bridges: A:V.98 Salt bridges: A:R.89 ACT.12: 4 residues within 4Å: Chain B: R.89, L.96, T.97, V.98 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.97 Water bridges: B:V.98 Salt bridges: B:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The structure of the Ca2+-binding, glycosylated F-spondin domain of F-spondin - A C2-domain variant in an extracellular matrix protein. Bmc Struct.Biol. (2011)

Release Date

2011-06-29

Peptides

Spondin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Spondin-1

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