SMTL ID : 2prr.2 (1 other biounit)

Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 12 residues within 4Å: Chain A: V.91, R.99, A.108, D.109, A.112, R.192 Chain E: V.91, G.95, R.99, A.108, D.109, R.192 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:R.99, E:D.109, A:R.99, A:R.192 Water bridges: E:R.99, E:R.192, A:R.99 PGE.5: 11 residues within 4Å: Chain B: V.91, R.99, A.108, D.109, A.112, R.192 Chain F: V.91, G.95, R.99, A.108, D.109 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:R.99, B:D.109, B:R.192, F:R.99, F:D.109 Water bridges: B:A.96, F:R.192 PGE.8: 12 residues within 4Å: Chain C: V.91, G.95, R.99, A.108, D.109, A.112 Chain D: V.91, G.95, R.99, A.108, D.109, R.192 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.99, C:D.109, D:R.99 Water bridges: C:V.92, C:R.99, D:R.99

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

PEG.2: 5 residues within 4Å: Chain A: P.8, S.10, G.180 Chain C: E.143 Chain E: K.117 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.180, E:K.117 Water bridges: A:R.182 PEG.3: 8 residues within 4Å: Chain A: V.41, F.55, H.59, Y.89, C.90, H.94, F.169, S.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.172 PEG.4: 6 residues within 4Å: Chain A: K.117 Chain E: P.8, S.10, R.11, G.180 Chain F: E.143 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: E:G.180, A:K.117 Water bridges: F:E.143 PEG.6: 6 residues within 4Å: Chain B: K.117 Chain E: E.143 Chain F: P.8, S.10, R.11, G.180 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:P.8, B:K.117 PEG.7: 7 residues within 4Å: Chain B: V.41, H.59, Y.89, C.90, H.94, F.169, S.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.172 PEG.9: 5 residues within 4Å: Chain A: E.143 Chain C: S.10, R.11, G.180 Chain D: K.117 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.117 PEG.10: 8 residues within 4Å: Chain C: V.41, F.42, H.59, Y.89, C.90, H.94, F.169, S.172 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.172 Water bridges: C:H.94 PEG.11: 4 residues within 4Å: Chain B: E.143, R.150, D.156 Chain D: R.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:E.143 Hydrogen bonds: D:R.11 PEG.12: 6 residues within 4Å: Chain B: E.143 Chain C: K.117 Chain D: P.8, S.10, R.11, G.180 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 interactions with chain C Water bridges: D:G.180, D:G.180, C:K.117 Hydrogen bonds: B:E.143, C:K.117 PEG.13: 7 residues within 4Å: Chain D: F.55, H.59, Y.89, C.90, H.94, F.169, S.172 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.172 PEG.14: 3 residues within 4Å: Chain E: P.5, A.6, H.7 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.6 PEG.15: 5 residues within 4Å: Chain E: F.42, H.59, H.94, F.169, S.172 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.172 PEG.16: 5 residues within 4Å: Chain B: S.10, I.179, G.180 Chain D: E.143 Chain F: K.117 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: F:K.117, B:G.180, D:E.143

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution. To be published

Release Date

2007-05-29

Peptides

Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

C
G

D
J

E
K

F
L

Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein

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