SMTL ID : 6f62.1

Crystal structure of the SYCP1 N-terminal head-to-head assembly in open conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: N.87, K.90 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: H.84, N.87 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain C: N.87, K.90 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: H.84, N.87 Ligand excluded by PLIP

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

MPD.3: 10 residues within 4Å: Chain A: L.12, E.15, A.16, I.19 Chain B: E.15, I.19 Chain C: L.5, Y.9 Chain D: V.8, L.12 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:V.8, A:I.19, C:L.5 MPD.4: 8 residues within 4Å: Chain B: Y.9, L.12, Y.13, A.16 Chain C: S.6, Y.9, S.10, Y.13 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.9, B:L.12, B:A.16, C:Y.9 Hydrogen bonds: C:S.10 MPD.7: 10 residues within 4Å: Chain A: L.5, Y.9 Chain B: V.8, L.12 Chain C: L.12, E.15, A.16, I.19 Chain D: E.15, I.19 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:I.19, A:L.5, B:V.8 MPD.8: 8 residues within 4Å: Chain A: S.6, Y.9, S.10, Y.13 Chain D: Y.9, L.12, Y.13, A.16 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.9, D:L.12, D:A.16, A:Y.9 Hydrogen bonds: A:S.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dunce, J.M. et al., Structural basis of meiotic chromosome synapsis through SYCP1 self-assembly. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-06-06

Peptides

Synaptonemal complex protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Synaptonemal complex protein 1