SMTL ID : 9doc.1

The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, at 1.2 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: H.19, L.22, Y.26, W.27, S.28, D.31, N.262, L.265 Ligands: MG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.31 Water bridges: A:N.262

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: R.15, A.18, R.21 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.15, A:R.21 PO4.3: 6 residues within 4Å: Chain A: A.121, E.122, R.150, I.153, S.154, L.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.150 Salt bridges: A:R.150

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 7 residues within 4Å: Chain A: D.101, S.103, S.105, V.106, T.169, T.198, D.199 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.101, A:S.103, A:D.199 MG.5: 1 residues within 4Å: Chain A: A.18 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: R.69 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain A: G.200, K.201, L.202, P.207, E.233, Q.236 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.200, H2O.6, H2O.8 MG.8: 3 residues within 4Å: Chain A: R.15, P.17, W.38 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: S.28, D.30, D.31 Ligands: GOL.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.28, H2O.9 MG.10: 2 residues within 4Å: Chain A: R.123, I.261 No protein-ligand interaction detected (PLIP)

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

NA.11: 1 residues within 4Å: Chain A: H.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.12 NA.12: 7 residues within 4Å: Chain A: D.95, Y.97, L.146, I.182, A.185, T.190, S.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.95, A:T.190 NA.13: 5 residues within 4Å: Chain A: I.143, L.144, K.155, G.156, D.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.143, A:D.159 Water bridges: A:G.156 NA.14: 4 residues within 4Å: Chain A: S.191, S.192, G.221, A.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.192, A:G.221 NA.15: 1 residues within 4Å: Chain A: R.239 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samarawickrama, P. et al., 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons. To be published

Release Date

2024-11-06

Peptides

Transcription factor ETV6,Capillary morphogenesis gene 2 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Transcription factor ETV6,Capillary morphogenesis gene 2 protein