SMTL ID : 7u68.1 (1 other biounit)

Crystal structure of the Vitronectin hemopexin-like domain binding Sodium-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: D.10, D.55, D.103, D.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.157 NA.2: 6 residues within 4Å: Chain A: F.12, A.57, A.105, A.159 Ligands: CL.3, SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.12

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

CL.3: 9 residues within 4Å: Chain A: A.11, F.12, A.56, A.57, A.104, A.105, A.158, A.159 Ligands: NA.2 Ligand excluded by PLIP

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

SO4.4: 14 residues within 4Å: Chain A: F.12, T.13, D.14, K.16, A.57, F.58, T.59, A.105, L.106, A.107, A.159, M.160, A.161 Ligands: NA.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.13, A:T.13, A:D.14, A:T.59, A:A.107, A:A.161 Salt bridges: A:K.16 SO4.5: 7 residues within 4Å: Chain A: Y.68, Y.75, R.77, Y.87, R.89, F.95, F.132 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.68, A:Y.75, A:Y.87 Water bridges: A:R.89 Salt bridges: A:R.77, A:R.89 SO4.6: 3 residues within 4Å: Chain A: G.124, K.125, Q.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.125, A:Q.126 Salt bridges: A:K.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, Y. et al., Structural basis for calcium-induced thermostability of human vitronectin. To Be Published

Release Date

2023-03-29

Peptides

vitronectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

vitronectin

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