SMTL ID : 7v6p.1

Crystal structure of human sNASP TPR domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: L.269, E.272, I.273 Chain B: E.209, Y.212 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.209, B:E.209, B:Y.212 GOL.2: 3 residues within 4Å: Chain A: E.140, W.143, S.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.179, A:S.179 GOL.3: 2 residues within 4Å: Chain A: Y.182, Y.220 No protein-ligand interaction detected (PLIP) GOL.4: 5 residues within 4Å: Chain A: E.201, H.203, R.241, Q.248 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.201, A:R.241, A:R.241, A:Q.248 Water bridges: A:D.204 GOL.5: 3 residues within 4Å: Chain A: Q.248 Chain B: Y.259 Ligands: GOL.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.259, B:Y.259, A:Q.248 GOL.10: 5 residues within 4Å: Chain A: E.209, Y.212 Chain B: L.269, E.272, I.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.209, A:Y.212 GOL.11: 3 residues within 4Å: Chain B: E.140, W.143, S.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.179, B:S.179 GOL.12: 2 residues within 4Å: Chain B: Y.182, Y.220 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.182 GOL.13: 5 residues within 4Å: Chain B: E.201, H.203, R.241, Q.248 Ligands: GOL.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.201, B:E.201, B:R.241, B:R.241, B:Q.248 GOL.14: 3 residues within 4Å: Chain A: Y.259 Chain B: Q.248 Ligands: GOL.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.248, A:Y.259, A:Y.259

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain A: E.275, D.279 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.275 CA.7: 1 residues within 4Å: Chain A: D.144 No protein-ligand interaction detected (PLIP) CA.15: 2 residues within 4Å: Chain B: E.275, D.279 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.275 CA.16: 1 residues within 4Å: Chain B: D.144 No protein-ligand interaction detected (PLIP)

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

PEG.8: 5 residues within 4Å: Chain A: D.3, K.7, L.10, E.46, E.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.3, A:K.7, A:E.49 PEG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.17: 5 residues within 4Å: Chain B: D.3, K.7, L.10, E.46, E.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.7, B:E.49 PEG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C.P. et al., Distinct histone H3-H4 binding modes of sNASP reveal the basis for cooperation and competition of histone chaperones. Genes Dev. (2021)

Release Date

2021-12-29

Peptides

Isoform 2 of Nuclear autoantigenic sperm protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Isoform 2 of Nuclear autoantigenic sperm protein

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