SMTL ID : 3bbf.1

Crystal structure of the NM23-H2 transcription factor complex with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 12 residues within 4Å: Chain A: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, V.111, G.112, N.114 Chain B: E.151 Ligands: MG.2 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.11, A:T.93, A:N.114, A:N.114, B:E.151 Water bridges: A:K.11, A:Y.51, A:Y.66, A:R.87, A:R.87, A:R.87, A:R.104, A:R.104, A:I.116, B:E.151, B:E.151, B:E.151 Salt bridges: A:R.87 pi-Stacking: A:F.59, A:F.59 GDP.3: 12 residues within 4Å: Chain B: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, V.111, G.112, N.114 Chain C: E.151 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.11, B:T.93, B:R.104, B:N.114, B:N.114, C:E.151 Water bridges: B:K.11, B:Y.51, B:R.104, B:R.104, B:H.117, B:G.118, C:E.151 Salt bridges: B:R.87 pi-Stacking: B:F.59, B:F.59 GDP.6: 13 residues within 4Å: Chain A: E.151 Chain C: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Ligands: MG.7 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.11, C:N.114, C:N.114, A:E.151 Water bridges: C:K.11, C:Y.51, C:R.87, C:R.87, C:R.87, C:R.87, C:R.104, C:R.104, C:R.104, C:R.104 Salt bridges: C:R.87, C:R.104 pi-Stacking: C:F.59, C:F.59 GDP.8: 13 residues within 4Å: Chain D: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Chain F: E.151 Ligands: MG.9 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.11, D:R.104, D:N.114, D:N.114, F:E.151 Water bridges: D:K.11, D:R.87, D:R.104, D:G.118 Salt bridges: D:R.87 pi-Stacking: D:F.59, D:F.59 GDP.10: 13 residues within 4Å: Chain D: E.151 Chain E: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Ligands: MG.11 21 PLIP interactions: 20 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.11, E:T.93, E:N.114, E:N.114, D:E.151 Water bridges: E:K.11, E:R.87, E:R.87, E:R.87, E:R.87, E:R.87, E:R.87, E:R.87, E:R.104, E:R.104, E:R.104, E:H.117 Salt bridges: E:R.87, E:R.104 pi-Stacking: E:F.59, E:F.59 GDP.12: 13 residues within 4Å: Chain E: E.151 Chain F: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Ligands: MG.13 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:K.11, F:R.104, F:N.114, F:N.114, E:E.151 Water bridges: F:K.11, F:R.87, F:R.87, F:R.87, F:R.104, F:R.104, F:G.112, F:H.117, F:H.117 Salt bridges: F:R.87 pi-Stacking: F:F.59, F:F.59

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: D.53 Ligands: GDP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: GDP.3 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: GDP.6 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain D: D.53 Ligands: GDP.8 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain E: D.120 Ligands: GDP.10 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain F: D.53 Ligands: GDP.12 No protein-ligand interaction detected (PLIP)

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.5: 8 residues within 4Å: Chain A: R.17 Chain B: C.144, A.145 Chain D: C.144, A.145 Chain E: Q.16, R.17, G.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:A.145 Water bridges: E:Q.16 DTT.14: 9 residues within 4Å: Chain B: Q.16, R.17, G.18 Chain C: C.144, A.145 Chain E: E.28, C.144, A.145 Chain F: R.17 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.15, B:V.15, B:Q.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dexheimer, T.S. et al., NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1. Mol.Cancer Ther. (2009)

Release Date

2008-09-23

Peptides

Nucleoside diphosphate kinase B: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase B

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