SMTL ID : 2ouw.1

Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: D.9, E.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.9, A:E.12 NA.8: 2 residues within 4Å: Chain C: D.9, E.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.9, C:E.12 NA.15: 2 residues within 4Å: Chain E: D.9, E.12 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.12

6 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.2: 9 residues within 4Å: Chain A: I.38, V.56, Y.75, Y.86, C.87, S.90, H.91 Chain B: T.118, N.119 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.90, A:H.91, B:T.118, B:T.118, B:N.119 Water bridges: A:N.36, A:W.39 UNL.5: 14 residues within 4Å: Chain A: T.118, N.119 Chain B: R.30, N.36, I.38, W.39, V.56, E.72, Y.75, Y.86, C.87, S.90, H.91 Ligands: ACY.7 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.30, B:R.30, B:N.36, B:W.39, B:Y.75, B:S.90, B:H.91, A:T.118, A:T.118, A:T.118, A:N.119 Water bridges: B:H.91, B:H.91 UNL.9: 9 residues within 4Å: Chain C: I.38, V.56, Y.75, Y.86, C.87, S.90, H.91 Chain D: T.118, N.119 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.75, C:S.90, C:S.90, C:H.91, C:H.91, D:T.118, D:T.118, D:N.119 Water bridges: C:N.36 UNL.12: 14 residues within 4Å: Chain C: T.118, N.119 Chain D: R.30, N.36, I.38, W.39, V.56, E.72, Y.75, Y.86, C.87, S.90, H.91 Ligands: ACY.14 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:T.118, C:T.118, C:N.119, D:R.30, D:R.30, D:N.36, D:W.39, D:E.72, D:S.90, D:S.90 Water bridges: D:H.91, D:H.91 UNL.16: 9 residues within 4Å: Chain E: I.38, V.56, Y.75, Y.86, C.87, S.90, H.91 Chain F: T.118, N.119 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:Y.75, E:S.90, F:T.118, F:T.118, F:N.119 Water bridges: E:N.36, E:N.36 UNL.19: 14 residues within 4Å: Chain E: T.118, N.119 Chain F: R.30, N.36, I.38, W.39, V.56, E.72, Y.75, Y.86, C.87, S.90, H.91 Ligands: ACY.21 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.30, F:R.30, F:N.36, F:W.39, F:E.72, F:S.90, F:S.90, F:H.91, F:H.91, E:T.118, E:T.118, E:N.119 Water bridges: F:H.91, F:H.91

12 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 3 residues within 4Å: Chain A: R.96, P.102, H.105 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.102 Water bridges: A:R.96, A:T.101 Salt bridges: A:R.96, A:H.105 ACY.4: 7 residues within 4Å: Chain A: V.5, G.41, N.44, D.45, L.48 Chain E: A.106, L.109 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:D.45, E:A.106, E:L.109 Hydrogen bonds: A:N.44 ACY.6: 6 residues within 4Å: Chain B: D.45, A.47, R.51 Chain D: A.106, E.107, A.110 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:A.110 Water bridges: D:E.107 Hydrogen bonds: B:D.45 Salt bridges: B:R.51 ACY.7: 6 residues within 4Å: Chain B: R.30, W.53, V.56, V.61, K.98 Ligands: UNL.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.61 Water bridges: B:K.98, B:K.98 Salt bridges: B:R.30, B:K.98 ACY.10: 3 residues within 4Å: Chain C: R.96, P.102, H.105 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.102 Water bridges: C:R.96, C:T.101 Salt bridges: C:R.96, C:H.105 ACY.11: 7 residues within 4Å: Chain A: A.106, L.109 Chain C: V.5, G.41, N.44, D.45, L.48 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.106, A:L.109, C:D.45 Hydrogen bonds: C:N.44 ACY.13: 6 residues within 4Å: Chain D: D.45, A.47, R.51 Chain F: A.106, E.107, A.110 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:A.110 Water bridges: F:E.107 Hydrogen bonds: D:D.45 Salt bridges: D:R.51 ACY.14: 6 residues within 4Å: Chain D: R.30, W.53, V.56, V.61, K.98 Ligands: UNL.12 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.61 Water bridges: D:K.98, D:K.98 Salt bridges: D:R.30, D:K.98 ACY.17: 3 residues within 4Å: Chain E: R.96, P.102, H.105 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:P.102 Water bridges: E:R.96, E:T.101 Salt bridges: E:R.96, E:H.105 ACY.18: 7 residues within 4Å: Chain C: A.106, L.109 Chain E: V.5, G.41, N.44, D.45, L.48 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:A.106, C:L.109, E:D.45 Hydrogen bonds: E:N.44 ACY.20: 6 residues within 4Å: Chain B: A.106, E.107, A.110 Chain F: D.45, A.47, R.51 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:A.110 Water bridges: B:E.107 Hydrogen bonds: F:D.45 Salt bridges: F:R.51 ACY.21: 6 residues within 4Å: Chain F: R.30, W.53, V.56, V.61, K.98 Ligands: UNL.19 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:V.61 Water bridges: F:K.98, F:K.98 Salt bridges: F:R.30, F:K.98

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution. To be published

Release Date

2007-03-06

Peptides

Alkylhydroperoxidase AhpD core: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Alkylhydroperoxidase AhpD core