SMTL ID : 5mey.1

Crystal structure of Smad4-MH1 bound to the GGCGC site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.66, C.110, C.122, H.127 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.110, A:C.122, A:H.127 ZN.14: 4 residues within 4Å: Chain C: C.66, C.110, C.122, H.127 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.66, C:C.110, C:C.122, C:H.127

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

CL.2: 5 residues within 4Å: Chain A: R.22, G.24, G.25, E.26, L.93 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.41, I.69, Q.70 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: H.106, A.113, F.114, D.115, Y.128 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: E.26, S.27, R.82 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain C: R.22, G.24, G.25, E.26, L.93 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: K.41, I.69, Q.70 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: H.106, A.113, F.114, D.115, Y.128 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: E.26, S.27, R.82 Ligand excluded by PLIP

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: E.48, C.66, T.68, Y.112, S.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.66, A:S.120 PEG.7: 1 residues within 4Å: Chain A: K.117 No protein-ligand interaction detected (PLIP) PEG.19: 5 residues within 4Å: Chain C: E.48, C.66, T.68, Y.112, S.120 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.66, C:S.120 PEG.20: 1 residues within 4Å: Chain C: K.117 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 4 residues within 4Å: Chain B: G.9, C.10, G.11 Ligands: EDO.21 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain D: G.9, C.10, G.11 Ligands: EDO.8 No protein-ligand interaction detected (PLIP)

10 x CA: CALCIUM ION(Non-functional Binders)

CA.9: 2 residues within 4Å: Chain B: G.6, G.7 No protein-ligand interaction detected (PLIP) CA.10: 3 residues within 4Å: Chain B: C.14, G.15 Chain D: G.5 No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain B: G.15, C.16 No protein-ligand interaction detected (PLIP) CA.12: 5 residues within 4Å: Chain B: G.15, C.16, A.17 Chain D: G.3, C.4 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain B: C.16, A.17, T.18 No protein-ligand interaction detected (PLIP) CA.22: 2 residues within 4Å: Chain D: G.6, G.7 No protein-ligand interaction detected (PLIP) CA.23: 3 residues within 4Å: Chain B: G.5 Chain D: C.14, G.15 No protein-ligand interaction detected (PLIP) CA.24: 2 residues within 4Å: Chain D: G.15, C.16 No protein-ligand interaction detected (PLIP) CA.25: 5 residues within 4Å: Chain B: G.3, C.4 Chain D: G.15, C.16, A.17 No protein-ligand interaction detected (PLIP) CA.26: 3 residues within 4Å: Chain D: C.16, A.17, T.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin-Malpartida, P. et al., Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors. Nat Commun (2017)

Release Date

2017-11-15

Peptides

MH1 domain of human Smad4: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

MH1 domain of human Smad4

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