SMTL ID : 1vcf.1 (2 other biounits)

Crystal Structure of IPP isomerase at I422

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-octamer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: D.135, D.136 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.135, A:D.136, A:D.136 CD.4: 2 residues within 4Å: Chain C: D.135, D.136 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.135, C:D.136, C:D.136 CD.7: 2 residues within 4Å: Chain E: D.135, D.136 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.135, E:D.136, E:D.136 CD.10: 2 residues within 4Å: Chain G: D.135, D.136 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.135, G:D.136, G:D.136

8 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.219 Hydrogen bonds: A:A.65, A:A.65, A:T.67, A:T.67, A:S.95, A:N.123, A:N.123, A:H.152, A:K.187, A:T.217, A:S.262, A:G.264, A:Y.266, A:A.285, A:R.286 pi-Stacking: A:W.219, A:W.219, A:W.219, A:W.219 FMN.3: 21 residues within 4Å: Chain B: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, V.222, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.222 Hydrogen bonds: B:A.65, B:A.65, B:T.67, B:S.95, B:N.123, B:N.123, B:K.187, B:K.187, B:T.217, B:S.262, B:G.264, B:A.285, B:R.286 pi-Stacking: B:W.219, B:W.219, B:W.219, B:W.219 FMN.5: 20 residues within 4Å: Chain C: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:W.219 Hydrogen bonds: C:A.65, C:A.65, C:T.67, C:T.67, C:S.95, C:N.123, C:N.123, C:H.152, C:K.187, C:T.217, C:S.262, C:G.264, C:Y.266, C:A.285, C:R.286 pi-Stacking: C:W.219, C:W.219, C:W.219, C:W.219 FMN.6: 21 residues within 4Å: Chain D: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, V.222, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:V.222 Hydrogen bonds: D:A.65, D:A.65, D:T.67, D:S.95, D:N.123, D:N.123, D:K.187, D:K.187, D:T.217, D:S.262, D:G.264, D:A.285, D:R.286 pi-Stacking: D:W.219, D:W.219, D:W.219, D:W.219 FMN.8: 20 residues within 4Å: Chain E: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:W.219 Hydrogen bonds: E:A.65, E:A.65, E:T.67, E:T.67, E:S.95, E:N.123, E:N.123, E:H.152, E:K.187, E:T.217, E:S.262, E:G.264, E:Y.266, E:A.285, E:R.286 pi-Stacking: E:W.219, E:W.219, E:W.219, E:W.219 FMN.9: 21 residues within 4Å: Chain F: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, V.222, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:V.222 Hydrogen bonds: F:A.65, F:A.65, F:T.67, F:S.95, F:N.123, F:N.123, F:K.187, F:K.187, F:T.217, F:S.262, F:G.264, F:A.285, F:R.286 pi-Stacking: F:W.219, F:W.219, F:W.219, F:W.219 FMN.11: 20 residues within 4Å: Chain G: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 20 PLIP interactions: 20 interactions with chain G Hydrophobic interactions: G:W.219 Hydrogen bonds: G:A.65, G:A.65, G:T.67, G:T.67, G:S.95, G:N.123, G:N.123, G:H.152, G:K.187, G:T.217, G:S.262, G:G.264, G:Y.266, G:A.285, G:R.286 pi-Stacking: G:W.219, G:W.219, G:W.219, G:W.219 FMN.12: 21 residues within 4Å: Chain H: A.65, M.66, T.67, G.94, S.95, N.123, H.152, K.187, V.189, G.190, T.217, W.219, V.222, S.262, G.263, G.264, Y.266, V.284, A.285, R.286, P.287 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:V.222 Hydrogen bonds: H:A.65, H:A.65, H:T.67, H:S.95, H:N.123, H:N.123, H:K.187, H:K.187, H:T.217, H:S.262, H:G.264, H:A.285, H:R.286 pi-Stacking: H:W.219, H:W.219, H:W.219, H:W.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wada, T. et al., Crystal Structure of IPP isomerase at I422. To be Published

Release Date

2005-04-19

Peptides

isopentenyl-diphosphate delta-isomerase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

isopentenyl-diphosphate delta-isomerase

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