SMTL ID : 6san.1

SALSA / DMBT1 / GP340 SRCR domain 8 soaked in calcium and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: S.54, W.55, D.56, D.59, V.93, R.94, C.95 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.54, A:D.56, A:D.59, A:V.93, H2O.3, H2O.3 MG.2: 3 residues within 4Å: Chain A: D.52, D.53, E.119 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.52, A:D.53, A:E.119, H2O.2, H2O.4 MG.3: 6 residues within 4Å: Chain A: D.53, D.91, D.92, N.108, N.114, C.115 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.53, A:D.91, A:D.91, A:D.92 MG.6: 7 residues within 4Å: Chain B: S.54, W.55, D.56, D.59, V.93, R.94, C.95 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.54, B:D.56, B:D.59, B:V.93, H2O.10, H2O.10 MG.7: 3 residues within 4Å: Chain B: D.52, D.53, E.119 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.53, B:E.119, H2O.9, H2O.10 MG.8: 6 residues within 4Å: Chain B: D.53, D.91, D.92, N.108, N.114, C.115 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.53, B:D.91, B:D.91, B:D.92

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: R.38, V.39, T.49, V.50, D.120, A.121 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: R.65, G.68, C.69, G.70 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: G.86, P.87, I.88, H.113, C.115, G.116, H.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.88, A:H.113 Water bridges: A:H.117 GOL.10: 3 residues within 4Å: Chain B: R.94, P.106, H.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reichhardt, M.P. et al., Structures of SALSA/DMBT1 SRCR domains reveal the conserved ligand-binding mechanism of the ancient SRCR fold. Life Sci Alliance (2020)

Release Date

2020-03-18

Peptides

Deleted in malignant brain tumors 1 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deleted in malignant brain tumors 1 protein

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