SMTL ID : 7txr.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 2 residues within 4Å: Chain A: I.164, R.176 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.164

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.10, D.55, D.103, D.157 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.55, A:D.103, H2O.2, H2O.2

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.4 Ligand excluded by PLIP

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

NA.4: 6 residues within 4Å: Chain A: F.12, A.57, A.105, A.159 Ligands: CL.3, SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.105

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

SO4.5: 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.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.12, A:D.14, A:T.59, A:A.107, A:A.107, A:A.161 Salt bridges: A:K.16

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
B

Vitronectin

Related Entries With Identical Sequence