SMTL ID : 4ej0.1 (10 other biounits)

Crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase from Burkholderia thailandensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-10-mer

Ligands

10 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 28 residues within 4Å: Chain A: T.18, G.19, G.22, F.23, I.24, D.44, N.45, R.48, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, N.180, V.181, H.188, K.189 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.178 Hydrogen bonds: A:G.19, A:F.23, A:I.24, A:N.45, A:R.48, A:K.51, A:K.66, A:E.87, A:A.89, A:S.91, A:N.104, A:N.104, A:K.155, A:V.181, A:V.181 Water bridges: A:G.25, A:Y.100, A:A.126 Salt bridges: A:K.51, A:K.66, A:H.188, A:K.189, A:K.189 pi-Stacking: A:Y.108 NAP.2: 27 residues within 4Å: Chain B: T.18, G.19, G.22, F.23, I.24, V.43, D.44, N.45, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, V.181, H.188, K.189 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.178 Hydrogen bonds: B:G.19, B:F.23, B:I.24, B:N.45, B:K.51, B:K.66, B:E.87, B:A.89, B:S.91, B:N.104, B:N.104, B:K.155, B:V.181, B:V.181 Water bridges: B:Y.100, B:K.189 Salt bridges: B:K.51, B:K.66, B:H.188, B:K.189, B:K.189 pi-Stacking: B:Y.178 NAP.3: 27 residues within 4Å: Chain C: T.18, G.19, G.22, F.23, I.24, V.43, D.44, N.45, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, V.181, H.188, K.189 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:Y.178 Hydrogen bonds: C:G.19, C:F.23, C:I.24, C:N.45, C:K.51, C:K.66, C:E.87, C:A.89, C:S.91, C:Y.100, C:N.104, C:N.104, C:Y.151, C:K.155, C:V.181, C:V.181, C:K.189 Water bridges: C:G.22, C:G.25 Salt bridges: C:K.51, C:K.66, C:H.188, C:K.189, C:K.189 pi-Stacking: C:Y.178 NAP.4: 25 residues within 4Å: Chain D: G.19, G.22, F.23, I.24, D.44, N.45, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, V.181, H.188, K.189 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:Y.178 Hydrogen bonds: D:G.19, D:F.23, D:I.24, D:N.45, D:R.48, D:K.51, D:E.87, D:A.89, D:S.91, D:N.104, D:N.104, D:Y.151, D:K.155, D:F.179, D:V.181 Salt bridges: D:K.51, D:K.66, D:H.188, D:K.189, D:K.189 pi-Stacking: D:Y.178 pi-Cation interactions: D:K.66 NAP.5: 28 residues within 4Å: Chain E: T.18, G.19, G.22, F.23, I.24, D.44, N.45, R.48, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, N.180, V.181, H.188, K.189 26 PLIP interactions: 26 interactions with chain E Hydrophobic interactions: E:Y.178 Hydrogen bonds: E:G.19, E:F.23, E:I.24, E:N.45, E:R.48, E:K.51, E:E.87, E:A.89, E:S.91, E:N.104, E:N.104, E:Y.151, E:K.155, E:V.181, E:V.181 Water bridges: E:G.25, E:K.189, E:K.189 Salt bridges: E:K.51, E:K.66, E:H.188, E:K.189, E:K.189 pi-Stacking: E:Y.108, E:Y.178 NAP.6: 28 residues within 4Å: Chain F: T.18, G.19, G.22, F.23, I.24, V.43, D.44, N.45, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, N.180, V.181, H.188, K.189 24 PLIP interactions: 24 interactions with chain F Hydrophobic interactions: F:Y.178 Hydrogen bonds: F:G.19, F:F.23, F:I.24, F:N.45, F:K.51, F:K.66, F:E.87, F:A.89, F:S.91, F:N.104, F:N.104, F:K.155, F:V.181, F:V.181, F:K.189 Water bridges: F:G.25, F:K.51 Salt bridges: F:K.51, F:K.66, F:H.188, F:K.189, F:K.189 pi-Stacking: F:Y.178 NAP.7: 28 residues within 4Å: Chain G: T.18, G.19, G.22, F.23, I.24, V.43, D.44, N.45, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, N.180, V.181, H.188, K.189 24 PLIP interactions: 24 interactions with chain G Hydrophobic interactions: G:Y.178 Hydrogen bonds: G:G.19, G:F.23, G:I.24, G:N.45, G:K.51, G:E.87, G:A.89, G:S.91, G:N.104, G:N.104, G:Y.151, G:K.155, G:V.181, G:V.181 Water bridges: G:G.25, G:K.189, G:K.189 Salt bridges: G:K.51, G:K.66, G:H.188, G:K.189, G:K.189 pi-Stacking: G:Y.178 NAP.8: 26 residues within 4Å: Chain H: G.19, G.22, F.23, I.24, D.44, N.45, R.48, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, V.181, H.188, K.189 25 PLIP interactions: 25 interactions with chain H Hydrophobic interactions: H:Y.178 Hydrogen bonds: H:G.19, H:F.23, H:I.24, H:N.45, H:R.48, H:K.51, H:K.66, H:E.87, H:A.89, H:S.91, H:N.104, H:N.104, H:Y.151, H:K.155, H:V.181, H:V.181 Water bridges: H:G.25, H:K.189, H:K.189 Salt bridges: H:K.51, H:K.66, H:H.188, H:K.189, H:K.189 NAP.9: 27 residues within 4Å: Chain I: T.18, G.19, G.22, F.23, I.24, V.43, D.44, N.45, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, V.181, H.188, K.189 23 PLIP interactions: 23 interactions with chain I Hydrophobic interactions: I:Y.178 Hydrogen bonds: I:G.19, I:F.23, I:I.24, I:N.45, I:K.51, I:K.66, I:E.87, I:A.89, I:S.91, I:N.104, I:N.104, I:K.155, I:F.179, I:V.181 Water bridges: I:G.25 Salt bridges: I:K.51, I:K.66, I:H.188, I:K.189, I:K.189 pi-Stacking: I:Y.108, I:Y.178 NAP.10: 25 residues within 4Å: Chain J: G.19, G.22, F.23, I.24, D.44, N.45, K.51, K.66, E.87, G.88, A.89, C.90, S.91, N.104, Y.108, A.126, S.127, S.128, Y.151, K.155, Y.178, F.179, V.181, H.188, K.189 22 PLIP interactions: 22 interactions with chain J Hydrophobic interactions: J:Y.178 Hydrogen bonds: J:G.19, J:F.23, J:I.24, J:N.45, J:K.51, J:E.87, J:A.89, J:S.91, J:N.104, J:N.104, J:K.155, J:V.181, J:V.181, J:K.189 Water bridges: J:G.25 Salt bridges: J:K.51, J:K.66, J:H.188, J:K.189, J:K.189 pi-Stacking: J:Y.178

Links

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Citation

Kim, M.S. et al., Structure and in silico substrate-binding mode of ADP-L-glycero-D-manno-heptose 6-epimerase from Burkholderia thailandensis. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-04-17

Peptides

ADP-L-glycero-D-manno-heptose-6-epimerase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

ADP-L-glycero-D-manno-heptose-6-epimerase

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