SMTL ID : 2prr.1 (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

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

PEG.1: 6 residues within 4Å: Chain A: P.8, S.10, R.11, G.180 Chain B: E.143 Chain C: K.117 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:K.117, B:E.143, B:E.143 Water bridges: A:G.180, A:G.180 PEG.2: 5 residues within 4Å: Chain A: K.117 Chain C: S.10, R.11, G.180 Chain D: E.143 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.117, C:G.180 PEG.3: 7 residues within 4Å: Chain A: V.41, 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.5: 7 residues within 4Å: Chain B: V.41, F.55, H.59, C.90, H.94, F.169, S.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.172, B:S.172 PEG.6: 6 residues within 4Å: Chain B: K.117 Chain E: E.143 Chain F: P.8, S.10, R.11, G.180 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, 1 interactions with chain B Water bridges: E:V.141, E:E.143, F:R.182 Hydrogen bonds: F:P.8, B:K.117 PEG.8: 8 residues within 4Å: Chain C: V.41, F.55, H.59, Y.89, C.90, H.94, F.169, S.172 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.172, C:S.172 Water bridges: C:Y.89 PEG.10: 5 residues within 4Å: Chain C: E.143 Chain D: S.10, R.11, G.180 Chain E: K.117 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.117, D:G.180 PEG.11: 8 residues within 4Å: Chain D: V.41, F.42, 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.12: 5 residues within 4Å: Chain D: K.117 Chain E: P.8, S.10, G.180 Chain F: E.143 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.117, E:G.180 PEG.14: 2 residues within 4Å: Chain E: E.151, H.152 2 PLIP interactions: 2 interactions with chain E Water bridges: E:H.152, E:H.152 PEG.15: 10 residues within 4Å: Chain E: P.39, V.41, F.42, F.55, H.59, Y.89, C.90, H.94, F.169, S.172 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.94, E:S.172 PEG.16: 8 residues within 4Å: Chain F: V.41, F.42, H.59, Y.89, C.90, H.94, F.169, S.172 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.172, F:S.172

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

PGE.4: 9 residues within 4Å: Chain B: V.91, R.99, A.108, D.109 Chain F: V.91, R.99, A.108, D.109, R.192 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:R.99, F:D.109, F:R.192, B:R.99, B:A.108 Water bridges: F:R.99, F:A.108, F:D.109, B:A.96, B:A.108 PGE.7: 13 residues within 4Å: Chain A: V.91, R.99, A.108, D.109, A.112, R.192 Chain C: V.91, G.95, R.99, A.108, D.109, A.112, R.192 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.99, A:D.109, A:R.192, C:R.99, C:R.192 Water bridges: A:R.99, C:A.96 PGE.9: 9 residues within 4Å: Chain D: V.91, R.99, A.108, D.109 Chain E: V.91, G.95, R.99, A.108, D.109 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:R.99, E:R.99, E:D.109, E:D.109 Water bridges: D:A.96, E:R.99 PGE.13: 4 residues within 4Å: Chain E: E.143, R.150, D.156 Chain F: R.11 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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
A

B
B

C
D

D
E

E
H

F
I

Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein

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