SMTL ID : 1m19.1

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

11 x MN: MANGANESE (II) ION(Non-functional Binders)(Non-covalent)

MN.1: 1 residues within 4Å: Chain A: G.134 No protein-ligand interaction detected (PLIP) MN.2: 2 residues within 4Å: Chain A: G.70, G.71 No protein-ligand interaction detected (PLIP) MN.3: 1 residues within 4Å: Chain A: C.88 No protein-ligand interaction detected (PLIP) MN.4: 1 residues within 4Å: Chain A: G.138 No protein-ligand interaction detected (PLIP) MN.5: 2 residues within 4Å: Chain A: T.38, G.39 No protein-ligand interaction detected (PLIP) MN.6: 2 residues within 4Å: Chain A: T.120, G.121 No protein-ligand interaction detected (PLIP) MN.29: 1 residues within 4Å: Chain B: G.134 No protein-ligand interaction detected (PLIP) MN.30: 2 residues within 4Å: Chain B: G.71, A.72 No protein-ligand interaction detected (PLIP) MN.31: 1 residues within 4Å: Chain B: G.121 No protein-ligand interaction detected (PLIP) MN.32: 1 residues within 4Å: Chain B: G.100 No protein-ligand interaction detected (PLIP) MN.66: 1 residues within 4Å: Chain G: D.77 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:D.77, H2O.16, H2O.17, H2O.17, H2O.20

5 x IMT: 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID(Non-functional Binders)

IMT.7: 5 residues within 4Å: Chain A: A.72, A.73 Ligands: PYB.8, PYB.15, BAL.16 No protein-ligand interaction detected (PLIP) IMT.18: 7 residues within 4Å: Chain B: T.32, G.33, T.34 Ligands: PYB.19, PYB.25, PYB.26, BAL.27 No protein-ligand interaction detected (PLIP) IMT.33: 6 residues within 4Å: Chain A: G.31, T.32 Ligands: PYB.34, PYB.40, PYB.41, BAL.42 No protein-ligand interaction detected (PLIP) IMT.44: 5 residues within 4Å: Chain B: T.104 Ligands: PYB.45, PYB.51, PYB.52, BAL.53 No protein-ligand interaction detected (PLIP) IMT.55: 4 residues within 4Å: Chain A: G.103, T.104 Ligands: PYB.56, PYB.63 No protein-ligand interaction detected (PLIP)

35 x PYB: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID(Non-functional Binders)

PYB.8: 8 residues within 4Å: Chain A: A.72, A.73, T.74 Ligands: IMT.7, PYB.9, PYB.13, PYB.14, PYB.15 No protein-ligand interaction detected (PLIP) PYB.9: 8 residues within 4Å: Chain A: A.73, T.74, T.75 Ligands: PYB.8, PYB.10, PYB.12, PYB.13, PYB.14 No protein-ligand interaction detected (PLIP) PYB.10: 7 residues within 4Å: Chain A: T.74, T.75, C.76 Ligands: PYB.9, ABU.11, PYB.12, PYB.13 No protein-ligand interaction detected (PLIP) PYB.12: 7 residues within 4Å: Chain B: A.73, T.74, T.75 Ligands: PYB.9, PYB.10, ABU.11, PYB.13 No protein-ligand interaction detected (PLIP) PYB.13: 8 residues within 4Å: Chain B: T.74, T.75, C.76 Ligands: PYB.8, PYB.9, PYB.10, PYB.12, PYB.14 No protein-ligand interaction detected (PLIP) PYB.14: 7 residues within 4Å: Chain B: T.75, C.76, C.77 Ligands: PYB.8, PYB.9, PYB.13, PYB.15 No protein-ligand interaction detected (PLIP) PYB.15: 8 residues within 4Å: Chain A: G.71 Chain B: C.76, C.77, G.78 Ligands: IMT.7, PYB.8, PYB.14, BAL.16 No protein-ligand interaction detected (PLIP) PYB.19: 8 residues within 4Å: Chain B: G.33, T.34, A.35 Ligands: IMT.18, PYB.20, PYB.24, PYB.25, PYB.26 No protein-ligand interaction detected (PLIP) PYB.20: 8 residues within 4Å: Chain A: A.113 Chain B: T.34, A.35, T.36 Ligands: PYB.19, PYB.21, PYB.24, PYB.25 No protein-ligand interaction detected (PLIP) PYB.21: 6 residues within 4Å: Chain B: T.36, T.37 Ligands: PYB.20, ABU.22, PYB.23, PYB.24 No protein-ligand interaction detected (PLIP) PYB.23: 6 residues within 4Å: Chain A: T.112, A.113, C.114 Ligands: PYB.21, ABU.22, PYB.24 No protein-ligand interaction detected (PLIP) PYB.24: 7 residues within 4Å: Chain A: A.113, C.114 Ligands: PYB.19, PYB.20, PYB.21, PYB.23, PYB.25 No protein-ligand interaction detected (PLIP) PYB.25: 9 residues within 4Å: Chain A: C.114, A.115, C.116 Chain B: G.33 Ligands: IMT.18, PYB.19, PYB.20, PYB.24, PYB.26 No protein-ligand interaction detected (PLIP) PYB.26: 8 residues within 4Å: Chain A: A.115, C.116, T.117 Chain B: G.33 Ligands: IMT.18, PYB.19, PYB.25, BAL.27 No protein-ligand interaction detected (PLIP) PYB.34: 7 residues within 4Å: Chain A: T.32, G.33 Ligands: IMT.33, PYB.35, PYB.39, PYB.40, PYB.41 No protein-ligand interaction detected (PLIP) PYB.35: 8 residues within 4Å: Chain A: G.33, T.34, A.35 Ligands: PYB.34, PYB.36, PYB.38, PYB.39, PYB.40 No protein-ligand interaction detected (PLIP) PYB.36: 7 residues within 4Å: Chain A: T.34, A.35, T.36 Ligands: PYB.35, ABU.37, PYB.38, PYB.39 No protein-ligand interaction detected (PLIP) PYB.38: 7 residues within 4Å: Chain B: A.113, C.114, A.115 Ligands: PYB.35, PYB.36, ABU.37, PYB.39 No protein-ligand interaction detected (PLIP) PYB.39: 9 residues within 4Å: Chain A: G.33 Chain B: C.114, A.115, C.116 Ligands: PYB.34, PYB.35, PYB.36, PYB.38, PYB.40 No protein-ligand interaction detected (PLIP) PYB.40: 8 residues within 4Å: Chain B: A.115, C.116, T.117 Ligands: IMT.33, PYB.34, PYB.35, PYB.39, PYB.41 No protein-ligand interaction detected (PLIP) PYB.41: 7 residues within 4Å: Chain B: C.116, T.117, T.118 Ligands: IMT.33, PYB.34, PYB.40, BAL.42 No protein-ligand interaction detected (PLIP) PYB.45: 7 residues within 4Å: Chain B: T.104, T.105, T.106 Ligands: IMT.44, PYB.46, PYB.51, PYB.52 No protein-ligand interaction detected (PLIP) PYB.46: 7 residues within 4Å: Chain B: T.105, T.106, C.107 Ligands: PYB.45, PYB.47, PYB.50, PYB.51 No protein-ligand interaction detected (PLIP) PYB.47: 7 residues within 4Å: Chain B: T.106, C.107, C.108 Ligands: PYB.46, ABU.48, PYB.49, PYB.50 No protein-ligand interaction detected (PLIP) PYB.49: 5 residues within 4Å: Chain A: A.41, A.42 Ligands: PYB.47, ABU.48, PYB.50 No protein-ligand interaction detected (PLIP) PYB.50: 6 residues within 4Å: Chain A: A.43, C.44 Ligands: PYB.46, PYB.47, PYB.49, PYB.51 No protein-ligand interaction detected (PLIP) PYB.51: 8 residues within 4Å: Chain A: A.43, C.44, T.45 Ligands: IMT.44, PYB.45, PYB.46, PYB.50, PYB.52 No protein-ligand interaction detected (PLIP) PYB.52: 8 residues within 4Å: Chain A: C.44, T.45, G.46 Chain B: G.103 Ligands: IMT.44, PYB.45, PYB.51, BAL.53 No protein-ligand interaction detected (PLIP) PYB.56: 7 residues within 4Å: Chain A: T.104, T.105, T.106 Ligands: IMT.55, PYB.57, PYB.62, PYB.63 No protein-ligand interaction detected (PLIP) PYB.57: 6 residues within 4Å: Chain A: T.105, T.106 Ligands: PYB.56, PYB.58, PYB.61, PYB.62 No protein-ligand interaction detected (PLIP) PYB.58: 7 residues within 4Å: Chain A: T.106, C.107, C.108 Ligands: PYB.57, ABU.59, PYB.60, PYB.61 No protein-ligand interaction detected (PLIP) PYB.60: 6 residues within 4Å: Chain B: A.41, A.42, A.43 Ligands: PYB.58, ABU.59, PYB.61 No protein-ligand interaction detected (PLIP) PYB.61: 7 residues within 4Å: Chain B: A.42, A.43, C.44 Ligands: PYB.57, PYB.58, PYB.60, PYB.62 No protein-ligand interaction detected (PLIP) PYB.62: 7 residues within 4Å: Chain B: A.43, C.44, T.45 Ligands: PYB.56, PYB.57, PYB.61, PYB.63 No protein-ligand interaction detected (PLIP) PYB.63: 8 residues within 4Å: Chain A: G.103 Chain B: C.44, T.45, G.46 Ligands: IMT.55, PYB.56, PYB.62, BAL.64 No protein-ligand interaction detected (PLIP)

5 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-functional Binders)

ABU.11: 6 residues within 4Å: Chain A: T.75, C.76 Chain B: A.73, T.74 Ligands: PYB.10, PYB.12 No protein-ligand interaction detected (PLIP) ABU.22: 5 residues within 4Å: Chain A: T.112 Chain B: T.36, T.37 Ligands: PYB.21, PYB.23 No protein-ligand interaction detected (PLIP) ABU.37: 6 residues within 4Å: Chain A: T.36 Chain B: T.112, A.113, C.114 Ligands: PYB.36, PYB.38 No protein-ligand interaction detected (PLIP) ABU.48: 6 residues within 4Å: Chain A: G.40, A.41, A.42 Chain B: C.107 Ligands: PYB.47, PYB.49 No protein-ligand interaction detected (PLIP) ABU.59: 4 residues within 4Å: Chain B: A.41, A.42 Ligands: PYB.58, PYB.60 No protein-ligand interaction detected (PLIP)

5 x BAL: BETA-ALANINE(Non-functional Binders)

BAL.16: 6 residues within 4Å: Chain A: G.70 Chain B: G.78, C.79 Ligands: IMT.7, PYB.15, DIB.17 No protein-ligand interaction detected (PLIP) BAL.27: 8 residues within 4Å: Chain A: A.115, C.116, T.117 Chain B: G.31, T.32 Ligands: IMT.18, PYB.26, DIB.28 No protein-ligand interaction detected (PLIP) BAL.42: 5 residues within 4Å: Chain B: T.118, T.119 Ligands: IMT.33, PYB.41, DIB.43 No protein-ligand interaction detected (PLIP) BAL.53: 7 residues within 4Å: Chain A: T.45, C.47 Chain B: A.102, G.103 Ligands: IMT.44, PYB.52, DIB.54 No protein-ligand interaction detected (PLIP) BAL.64: 6 residues within 4Å: Chain A: G.103 Chain B: T.45, G.46, C.47 Ligands: PYB.63, DIB.65 No protein-ligand interaction detected (PLIP)

5 x DIB: 3-AMINO-(DIMETHYLPROPYLAMINE)(Non-functional Binders)(Non-covalent)

DIB.17: 6 residues within 4Å: Chain A: G.70, G.71 Chain B: G.78, T.80, G.81 Ligands: BAL.16 No protein-ligand interaction detected (PLIP) DIB.28: 7 residues within 4Å: Chain A: T.117, T.118, T.119 Chain B: A.30, G.31, T.32 Ligands: BAL.27 No protein-ligand interaction detected (PLIP) DIB.43: 4 residues within 4Å: Chain B: T.119, T.120 Chain E: A.14 Ligands: BAL.42 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.14 DIB.54: 3 residues within 4Å: Chain A: C.47, T.48 Ligands: BAL.53 No protein-ligand interaction detected (PLIP) DIB.65: 5 residues within 4Å: Chain A: A.102 Chain B: G.46, T.48, C.49 Ligands: BAL.64 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suto, R.K. et al., Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands. J.Mol.Biol. (2003)

Release Date

2003-02-18

Peptides

Histone H3.3C: CG
Histone H4: DH
Histone H2A type 1: EI
Histone H2B: FJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

G
E

D
B

H
F

E
C

I
G

F
D

J
H

Histone H3.3C

Histone H4

Histone H2A type 1

Histone H2B

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