SMTL ID : 2x86.3 (3 other biounits)

AGME bound to ADP-B-mannose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-pentamer

Ligands

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

NAP.1: 30 residues within 4Å: Chain A: T.52, G.53, G.56, F.57, I.58, V.77, D.78, N.79, K.85, K.100, E.122, G.123, A.124, C.125, S.126, Y.135, N.139, Y.143, A.161, S.162, S.163, F.187, K.191, Y.214, F.215, N.216, V.217, H.224, K.225 Ligands: BMA.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.214 Hydrogen bonds: A:G.53, A:F.57, A:I.58, A:N.79, A:K.100, A:E.122, A:A.124, A:A.124, A:S.126, A:Y.135, A:N.139, A:N.139, A:K.191, A:V.217 Water bridges: A:G.59, A:S.126, A:K.225, A:K.225 Salt bridges: A:K.85, A:K.100, A:H.224, A:K.225, A:K.225 pi-Stacking: A:Y.143, A:Y.214 NAP.4: 30 residues within 4Å: Chain B: T.52, G.53, G.56, F.57, I.58, V.77, D.78, N.79, K.85, K.100, E.122, G.123, A.124, C.125, S.126, Y.135, N.139, Y.143, A.161, S.162, S.163, F.187, K.191, Y.214, F.215, N.216, V.217, H.224, K.225 Ligands: BMA.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.214 Hydrogen bonds: B:G.53, B:F.57, B:I.58, B:N.79, B:K.100, B:E.122, B:A.124, B:S.126, B:Y.135, B:N.139, B:N.139, B:K.191, B:V.217 Water bridges: B:K.85, B:S.126, B:S.126, B:H.224 Salt bridges: B:K.85, B:K.100, B:H.224, B:K.225, B:K.225 pi-Stacking: B:Y.143, B:Y.214 NAP.7: 29 residues within 4Å: Chain C: T.52, G.53, G.56, F.57, I.58, V.77, D.78, N.79, K.85, K.100, E.122, G.123, A.124, C.125, S.126, Y.135, N.139, Y.143, A.161, S.162, S.163, F.187, K.191, Y.214, F.215, V.217, H.224, K.225 Ligands: BMA.9 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:Y.214, C:V.217 Hydrogen bonds: C:G.53, C:F.57, C:I.58, C:N.79, C:K.100, C:E.122, C:A.124, C:S.126, C:Y.135, C:N.139, C:N.139, C:K.191, C:V.217, C:K.225 Water bridges: C:G.59, C:K.85, C:K.85 Salt bridges: C:K.85, C:K.100, C:H.224, C:K.225, C:K.225 pi-Stacking: C:Y.143, C:Y.214 pi-Cation interactions: C:K.100 NAP.10: 30 residues within 4Å: Chain D: T.52, G.53, G.56, F.57, I.58, V.77, D.78, N.79, K.85, K.100, E.122, G.123, A.124, C.125, S.126, Y.135, N.139, Y.143, A.161, S.162, S.163, F.187, K.191, Y.214, F.215, N.216, V.217, H.224, K.225 Ligands: BMA.12 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:Y.214 Hydrogen bonds: D:G.53, D:F.57, D:I.58, D:N.79, D:K.100, D:E.122, D:A.124, D:S.126, D:Y.135, D:N.139, D:N.139, D:K.191, D:V.217 Water bridges: D:N.79, D:A.124, D:S.126 Salt bridges: D:K.85, D:K.100, D:H.224, D:K.225, D:K.225 pi-Stacking: D:Y.143, D:Y.214 pi-Cation interactions: D:K.100 NAP.13: 28 residues within 4Å: Chain E: G.53, G.56, F.57, I.58, V.77, D.78, N.79, K.85, K.100, E.122, G.123, A.124, C.125, S.126, Y.135, N.139, Y.143, A.161, S.162, S.163, F.187, K.191, Y.214, F.215, V.217, H.224, K.225 Ligands: BMA.15 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:Y.214 Hydrogen bonds: E:G.53, E:F.57, E:I.58, E:N.79, E:K.100, E:E.122, E:A.124, E:S.126, E:Y.135, E:N.139, E:N.139, E:K.191, E:V.217 Water bridges: E:S.126, E:S.126 Salt bridges: E:K.85, E:K.100, E:H.224, E:K.225, E:K.225 pi-Stacking: E:Y.214 pi-Cation interactions: E:K.100

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 16 residues within 4Å: Chain A: T.128, N.216, S.227, M.228, A.229, V.231, H.234, L.247, F.248, S.251, F.254, R.256, F.290, L.315, Y.319 Ligands: BMA.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.128, A:N.216, A:A.229, A:F.248, A:S.251, A:S.251, A:Y.319 Salt bridges: A:R.256, A:R.256 pi-Stacking: A:F.248 ADP.5: 16 residues within 4Å: Chain B: T.128, N.216, S.227, M.228, A.229, V.231, H.234, L.247, F.248, S.251, F.254, R.256, F.290, L.315, Y.319 Ligands: BMA.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.128, B:N.216, B:A.229, B:F.248, B:S.251, B:S.251, B:Y.319 Salt bridges: B:R.256, B:R.256 pi-Stacking: B:F.248, B:F.248 ADP.8: 15 residues within 4Å: Chain C: T.128, N.216, S.227, A.229, V.231, H.234, L.247, F.248, S.251, F.254, R.256, F.290, L.315, Y.319 Ligands: BMA.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.128, C:N.216, C:A.229, C:H.234, C:F.248, C:S.251, C:Y.319, C:Y.319 Salt bridges: C:R.256, C:R.256 pi-Stacking: C:F.248, C:F.248 ADP.11: 16 residues within 4Å: Chain D: T.128, N.216, S.227, M.228, A.229, V.231, H.234, L.247, F.248, S.251, F.254, R.256, F.290, L.315, Y.319 Ligands: BMA.12 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.216, D:A.229, D:F.248, D:S.251, D:Y.319, D:Y.319 Water bridges: D:F.215, D:R.256 Salt bridges: D:R.256, D:R.256 pi-Stacking: D:F.248, D:F.248 ADP.14: 16 residues within 4Å: Chain E: T.128, N.216, S.227, M.228, A.229, V.231, H.234, L.247, F.248, S.251, F.254, R.256, F.290, L.315, Y.319 Ligands: BMA.15 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:N.216, E:N.216, E:A.229, E:F.248, E:S.251, E:S.251, E:Y.319 Salt bridges: E:R.256, E:R.256 pi-Stacking: E:F.248, E:F.248

5 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.3: 8 residues within 4Å: Chain A: S.126, T.128, S.163, F.187, K.225, M.228 Ligands: NAP.1, ADP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.163, A:S.163, A:K.225, A:M.228 Water bridges: A:Q.320 BMA.6: 8 residues within 4Å: Chain B: S.126, T.128, S.163, F.187, K.225, M.228 Ligands: NAP.4, ADP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.163, B:K.225, B:M.228 BMA.9: 7 residues within 4Å: Chain C: S.126, S.163, F.187, K.225, M.228 Ligands: NAP.7, ADP.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.163, C:K.225, C:M.228 BMA.12: 9 residues within 4Å: Chain D: S.126, T.128, S.163, F.187, F.215, K.225, M.228 Ligands: NAP.10, ADP.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.163, D:K.225, D:M.228 BMA.15: 8 residues within 4Å: Chain E: S.126, T.128, S.163, F.187, K.225, M.228 Ligands: NAP.13, ADP.14 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.163, E:K.225, E:M.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kowatz, T. et al., The Crystal Structure of the Y140F Mutant of Adp-L-Glycero-D-Manno-Heptose 6-Epimerase Bound to Adp-Beta-D-Mannose Suggests a One Base Mechanism. Protein Sci. (2010)

Release Date

2010-03-16

Peptides

ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

E
O

ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE

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