SMTL ID : 6hk9.1

Crystal structure of TEX12 F102A F109E V116A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

14 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.7, A.8 Chain C: D.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.7, H2O.1, H2O.1 CA.2: 4 residues within 4Å: Chain A: E.7, K.11, D.12, D.15 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.7, A:D.12, A:D.15, H2O.3, H2O.3, H2O.3 CA.3: 3 residues within 4Å: Chain A: N.53, E.56, N.57 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.56 CA.6: 3 residues within 4Å: Chain B: N.53, E.56, N.57 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.56 CA.7: 2 residues within 4Å: Chain B: D.43 Ligands: CA.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.43, H2O.5, H2O.5 CA.8: 3 residues within 4Å: Chain B: D.43, E.47 Ligands: CA.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.43, B:D.43, B:E.47, H2O.5, H2O.6 CA.9: 5 residues within 4Å: Chain B: D.12, D.15 Chain D: K.11, D.15 Ligands: CA.19 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.15, B:D.12, B:D.15, H2O.6, H2O.15 CA.11: 3 residues within 4Å: Chain A: D.6 Chain C: E.7, A.8 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.7, H2O.8, H2O.8 CA.12: 4 residues within 4Å: Chain C: E.7, K.11, D.12, D.15 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.7, C:D.12, C:D.15, H2O.10, H2O.11, H2O.11 CA.13: 3 residues within 4Å: Chain C: N.53, E.56, N.57 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.56 CA.16: 3 residues within 4Å: Chain D: N.53, E.56, N.57 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.56 CA.17: 2 residues within 4Å: Chain D: D.43 Ligands: CA.18 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.43, H2O.12, H2O.13 CA.18: 3 residues within 4Å: Chain D: D.43, E.47 Ligands: CA.17 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.43, D:D.43, D:E.47, H2O.12, H2O.14 CA.19: 5 residues within 4Å: Chain B: K.11, D.15 Chain D: D.12, D.15 Ligands: CA.9 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.15, D:D.12, D:D.15, H2O.7, H2O.14

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain A: R.63, L.66, R.67, F.70 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.67 ACT.5: 4 residues within 4Å: Chain A: S.40, Y.41, E.44 Chain B: M.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.41 Hydrogen bonds: A:S.40 ACT.14: 4 residues within 4Å: Chain C: R.63, L.66, R.67, F.70 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.67 ACT.15: 4 residues within 4Å: Chain C: S.40, Y.41, E.44 Chain D: M.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.41 Hydrogen bonds: C:S.40

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.10: 4 residues within 4Å: Chain B: R.67, F.70, T.71, A.74 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.70, B:A.74 MRD.20: 4 residues within 4Å: Chain D: R.67, F.70, T.71, A.74 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.70, D:A.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salmon, L.J. et al., Synaptonemal complex central element extension through hierarchical assembly of SYCE2-TEX12 into alpha-fibres. To Be Published

Release Date

2019-09-18

Peptides

Testis-expressed protein 12: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Testis-expressed protein 12

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