SMTL ID : 9e9g.1

Heligmosomoides polygyrus TGF-beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human TGF-beta Type II Receptor Extracellular Domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: C.25, D.26, N.27, Q.28, C.31, W.52, F.98, F.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:Q.28, A:Q.28 Water bridges: A:E.89 GOL.2: 2 residues within 4Å: Chain A: R.21, F.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.22 GOL.3: 4 residues within 4Å: Chain A: E.78, D.79, A.81, S.82 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.82 GOL.4: 5 residues within 4Å: Chain A: K.10, Q.45, E.46, V.47, P.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.45 Water bridges: A:K.69 GOL.5: 5 residues within 4Å: Chain A: A.81, S.82, P.83, S.103, S.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.103, A:S.103, A:S.103 GOL.6: 4 residues within 4Å: Chain A: E.62, Y.72, H.73, D.74 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.72, A:H.73 Water bridges: A:P.71, A:H.73, A:D.74 GOL.14: 10 residues within 4Å: Chain A: E.42 Chain B: R.28, E.64, V.66, Y.83, P.84, R.85, I.86, A.87 Ligands: NA.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.28, B:R.28, B:P.84 GOL.15: 6 residues within 4Å: Chain B: P.10, L.11, D.13, W.18, Y.19, Y.21 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.11, B:D.13, B:Y.19, B:Y.19, B:Y.21 Water bridges: B:D.13

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

CL.7: 6 residues within 4Å: Chain A: K.91, K.92, E.95, T.96 Ligands: NA.8, NA.10 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: P.45, N.46, C.69, Y.70, Q.71 Ligand excluded by PLIP

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

NA.8: 5 residues within 4Å: Chain A: K.92, G.94, E.95, T.96 Ligands: CL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.95, A:E.95 NA.9: 4 residues within 4Å: Chain A: E.42 Chain B: R.28, P.84 Ligands: GOL.14 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.42, B:R.28 Water bridges: B:R.85, B:R.85 NA.10: 8 residues within 4Å: Chain A: E.89, K.90, K.91, K.92, E.95, T.96, F.97 Ligands: CL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.89, A:E.95, A:F.97 NA.11: 1 residues within 4Å: Chain A: D.74 No protein-ligand interaction detected (PLIP) NA.17: 5 residues within 4Å: Chain B: R.28, H.29, R.50, E.64, F.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.50, B:F.65 Water bridges: B:H.29

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.12: 8 residues within 4Å: Chain A: F.17, E.46, V.64, C.65, H.66, D.67, Y.72 Chain B: R.85 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.85, A:D.67 Hydrogen bonds: A:H.66 CAC.13: 10 residues within 4Å: Chain A: F.75, I.76, L.77, E.78, D.79, K.88, K.90, M.99, C.100, S.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, S.E. et al., Heligmosomoides polygyrus TGF-beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human TGF-beta Type II Receptor Extracellular Domain. To Be Published

Release Date

2025-01-22

Peptides

TGF-beta receptor type-2: A
Transforming growth factor beta mimic 6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TGF-beta receptor type-2

Transforming growth factor beta mimic 6