SMTL ID : 6f0h.1

Crystal structure ASF1-ip4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-6-6-mer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: N.116, E.118, R.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.116, A:E.118 Water bridges: A:R.125 Salt bridges: A:R.125 SO4.2: 3 residues within 4Å: Chain A: R.71, H.72, M.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.73 Salt bridges: A:H.72 SO4.4: 6 residues within 4Å: Chain A: R.110 Chain B: R.12, R.13, G.16 Chain G: R.147 Chain H: T.21 12 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, 2 interactions with chain G Water bridges: A:R.110, A:R.110, A:R.110, A:R.110, B:R.12, B:R.12, B:R.12, G:R.147 Salt bridges: A:R.110, B:R.12, B:R.13, G:R.147 SO4.7: 6 residues within 4Å: Chain A: R.147 Chain B: T.21 Chain C: R.110 Chain D: R.12, R.13, G.16 11 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C, 2 interactions with chain A Water bridges: D:R.12, D:R.12, C:R.110, C:R.110, C:R.110, C:R.110, A:R.147 Salt bridges: D:R.12, D:R.13, C:R.110, A:R.147 SO4.8: 3 residues within 4Å: Chain E: N.116, E.118, R.125 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.116, E:E.118 Water bridges: E:R.125 Salt bridges: E:R.125 SO4.9: 3 residues within 4Å: Chain E: R.71, H.72, M.73 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:M.73 Salt bridges: E:H.72 SO4.11: 6 residues within 4Å: Chain E: R.110 Chain F: R.12, R.13, G.16 Chain K: R.147 Chain L: T.21 12 PLIP interactions: 5 interactions with chain F, 2 interactions with chain K, 5 interactions with chain E Water bridges: F:R.12, F:R.12, F:R.12, K:R.147, E:R.110, E:R.110, E:R.110, E:R.110 Salt bridges: F:R.12, F:R.13, K:R.147, E:R.110 SO4.14: 6 residues within 4Å: Chain E: R.147 Chain F: T.21 Chain G: R.110 Chain H: R.12, R.13, G.16 11 PLIP interactions: 4 interactions with chain H, 5 interactions with chain G, 2 interactions with chain E Water bridges: H:R.12, H:R.12, G:R.110, G:R.110, G:R.110, G:R.110, E:R.147 Salt bridges: H:R.12, H:R.13, G:R.110, E:R.147 SO4.15: 3 residues within 4Å: Chain I: N.116, E.118, R.125 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:N.116, I:E.118 Water bridges: I:R.125 Salt bridges: I:R.125 SO4.16: 3 residues within 4Å: Chain I: R.71, H.72, M.73 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:M.73 Salt bridges: I:H.72 SO4.18: 6 residues within 4Å: Chain C: R.147 Chain D: T.21 Chain I: R.110 Chain J: R.12, R.13, G.16 12 PLIP interactions: 5 interactions with chain J, 5 interactions with chain I, 2 interactions with chain C Water bridges: J:R.12, J:R.12, J:R.12, I:R.110, I:R.110, I:R.110, I:R.110, C:R.147 Salt bridges: J:R.12, J:R.13, I:R.110, C:R.147 SO4.21: 6 residues within 4Å: Chain I: R.147 Chain J: T.21 Chain K: R.110 Chain L: R.12, R.13, G.16 11 PLIP interactions: 4 interactions with chain L, 5 interactions with chain K, 2 interactions with chain I Water bridges: L:R.12, L:R.12, K:R.110, K:R.110, K:R.110, K:R.110, I:R.147 Salt bridges: L:R.12, L:R.13, K:R.110, I:R.147

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: L.59, D.79, A.80, P.81, N.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.57, A:L.59, A:N.82, A:N.82 GOL.5: 1 residues within 4Å: Chain C: D.79 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain E: L.59, D.79, A.80, P.81, N.82 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.57, E:L.59, E:N.82, E:N.82 GOL.12: 1 residues within 4Å: Chain G: D.79 No protein-ligand interaction detected (PLIP) GOL.17: 5 residues within 4Å: Chain I: L.59, D.79, A.80, P.81, N.82 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:Q.57, I:L.59, I:N.82, I:N.82 GOL.19: 1 residues within 4Å: Chain K: D.79 No protein-ligand interaction detected (PLIP)

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 5 residues within 4Å: Chain C: Y.21, P.83, G.84, K.131, F.134 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.21, C:K.131 Water bridges: C:K.131, C:P.132, C:F.134, C:F.134, C:S.135 Salt bridges: C:K.131 CIT.13: 5 residues within 4Å: Chain G: Y.21, P.83, G.84, K.131, F.134 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:Y.21, G:K.131 Water bridges: G:K.131, G:P.132, G:F.134, G:F.134, G:S.135 Salt bridges: G:K.131 CIT.20: 5 residues within 4Å: Chain K: Y.21, P.83, G.84, K.131, F.134 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:Y.21, K:K.131 Water bridges: K:K.131, K:P.132, K:F.134, K:F.134, K:S.135 Salt bridges: K:K.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bakail, M. et al., Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1. Cell Chem Biol (2019)

Release Date

2019-06-12

Peptides

Histone chaperone ASF1A: ACEGIK
ip4: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

I
A

K
C

B
B

D
D

F
B

H
D

J
B

L
D

Histone chaperone ASF1A

ip4

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