SMTL ID : 1ne7.1

HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-hexamer

Ligands

6 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 4 residues within 4Å: Chain A: R.23, Q.26, F.27, K.33 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.23, A:K.33, A:E.132, A:R.234, A:R.234 GLC-GLC.2: 3 residues within 4Å: Chain B: Q.26, F.27, K.33 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.132, B:R.234, B:R.234 GLC-GLC.3: 5 residues within 4Å: Chain C: R.23, Q.26, F.27, K.33, E.132 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.23, C:K.33, C:E.132, C:R.234, C:R.234 GLC-GLC.4: 3 residues within 4Å: Chain D: Q.26, F.27, K.33 5 PLIP interactions: 5 interactions with chain D Water bridges: D:R.23, D:R.23, D:R.23, D:K.33, D:R.234 GLC-GLC.5: 3 residues within 4Å: Chain E: Q.26, F.27, K.33 4 PLIP interactions: 4 interactions with chain E Water bridges: E:R.23, E:R.23, E:E.132, E:R.234 GLC-GLC.6: 3 residues within 4Å: Chain F: Q.26, F.27, K.33 4 PLIP interactions: 4 interactions with chain F Water bridges: F:R.23, F:R.23, F:E.132, F:R.234

6 x 16G: 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

16G.7: 11 residues within 4Å: Chain A: S.151, S.152, R.158, V.159, K.160, T.161, M.184 Chain C: M.1, K.2, L.258, H.262 14 PLIP interactions: 4 interactions with chain C, 10 interactions with chain A Hydrogen bonds: C:M.1, A:S.151, A:S.152, A:R.158, A:V.159, A:T.161 Water bridges: C:H.262, A:S.152 Salt bridges: C:K.2, C:H.262, A:R.158, A:K.160, A:K.160 Hydrophobic interactions: A:V.159 16G.10: 11 residues within 4Å: Chain A: M.1, K.2, L.258, H.262 Chain B: S.151, S.152, R.158, V.159, K.160, T.161, M.184 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.159 Hydrogen bonds: B:S.151, B:S.152, B:R.158, B:V.159, B:T.161 Water bridges: B:S.152, A:M.1, A:K.2, A:K.2, A:P.233 Salt bridges: B:R.158, B:K.160, A:K.2, A:H.262 16G.13: 11 residues within 4Å: Chain B: M.1, K.2, L.258, H.262 Chain C: S.151, S.152, R.158, V.159, K.160, T.161, M.184 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.151, C:S.152, C:R.158, C:V.159, C:T.161, C:T.161 Water bridges: C:S.152, C:V.159 Salt bridges: C:R.158, C:K.160, C:K.160, B:K.2, B:H.262 16G.17: 11 residues within 4Å: Chain D: S.151, S.152, R.158, V.159, K.160, T.161, M.184 Chain F: M.1, K.2, L.258, H.262 12 PLIP interactions: 2 interactions with chain F, 10 interactions with chain D Salt bridges: F:K.2, F:H.262, D:R.158, D:K.160, D:K.160 Hydrogen bonds: D:S.151, D:S.152, D:V.159, D:T.161, D:T.161 Water bridges: D:S.152, D:V.159 16G.20: 10 residues within 4Å: Chain D: M.1, K.2, H.262 Chain E: S.151, S.152, R.158, V.159, K.160, T.161, M.184 14 PLIP interactions: 9 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:V.159 Hydrogen bonds: E:S.151, E:S.152, E:V.159, E:T.161, E:T.161, D:M.1 Water bridges: E:S.152, D:M.1, D:P.233 Salt bridges: E:R.158, E:K.160, D:K.2, D:H.262 16G.23: 10 residues within 4Å: Chain E: M.1, K.2, H.262 Chain F: S.151, S.152, R.158, V.159, K.160, T.161, M.184 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain F Hydrogen bonds: E:M.1, F:S.151, F:S.152, F:R.158, F:V.159, F:T.161 Water bridges: E:K.2, F:S.152 Salt bridges: E:K.2, E:H.262, F:R.158, F:K.160 Hydrophobic interactions: F:V.159

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 7 residues within 4Å: Chain A: T.41, G.42, S.43, T.44, P.45, K.208 Ligands: AGP.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.43, A:T.44, A:T.44, A:R.172 Salt bridges: A:K.208 SO4.11: 7 residues within 4Å: Chain B: T.41, G.42, S.43, T.44, P.45, K.208 Ligands: AGP.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.43, B:T.44 Water bridges: B:S.43, B:T.44, B:K.208 Salt bridges: B:K.208 SO4.14: 8 residues within 4Å: Chain C: T.41, G.42, S.43, T.44, P.45, R.172, K.208 Ligands: AGP.16 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.43, C:T.44, C:T.44, C:R.172 Water bridges: C:S.43, C:S.43, C:T.44 Salt bridges: C:K.208 SO4.15: 3 residues within 4Å: Chain C: R.21, Y.55, D.60 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.21, C:D.60 Salt bridges: C:R.21 SO4.18: 8 residues within 4Å: Chain D: T.41, G.42, S.43, T.44, P.45, R.172, K.208 Ligands: AGP.19 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.43, D:T.44, D:R.172 Water bridges: D:T.44, D:T.44, D:R.172, D:K.208 Salt bridges: D:K.208 SO4.21: 6 residues within 4Å: Chain E: T.41, G.42, S.43, T.44, K.208 Ligands: AGP.22 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.43, E:T.44, E:T.44, E:T.44 Water bridges: E:K.208, E:K.208 Salt bridges: E:K.208 SO4.24: 8 residues within 4Å: Chain F: T.41, G.42, S.43, T.44, P.45, R.172, K.208 Ligands: AGP.25 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.43, F:T.44, F:T.44, F:T.44, F:R.172, F:R.172 Water bridges: F:N.170, F:K.208, F:K.208, F:K.208, F:K.208, F:K.208 Salt bridges: F:K.208

6 x AGP: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE(Non-covalent)

AGP.9: 15 residues within 4Å: Chain A: P.40, T.41, G.42, S.43, T.44, M.71, D.72, G.137, I.138, G.139, H.143, A.145, F.146, K.208 Ligands: SO4.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.41, A:T.41, A:T.41, A:S.43, A:T.44, A:T.44, A:D.72, A:G.137, A:H.143, A:A.145 Water bridges: A:N.170 Salt bridges: A:K.208 AGP.12: 16 residues within 4Å: Chain B: T.41, G.42, S.43, T.44, P.45, M.71, D.72, Y.85, G.137, I.138, G.139, H.143, A.145, F.146, K.208 Ligands: SO4.11 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.43, B:T.44, B:D.72, B:Y.85, B:Y.85, B:H.143, B:A.145, B:A.145 Water bridges: B:T.41, B:T.41, B:T.41, B:S.43, B:S.43, B:T.44, B:T.44, B:G.137, B:N.170, B:K.208 Salt bridges: B:K.208 AGP.16: 15 residues within 4Å: Chain C: T.41, G.42, S.43, T.44, P.45, D.72, Y.85, G.139, H.143, A.145, F.146, T.166, N.170, K.208 Ligands: SO4.14 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.41, C:S.43, C:T.44, C:D.72, C:Y.85, C:H.143, C:A.145, C:A.145, C:N.170, C:N.170 Water bridges: C:T.41, C:S.43, C:S.43, C:R.172, C:R.172 Salt bridges: C:K.208 AGP.19: 16 residues within 4Å: Chain D: T.41, G.42, S.43, T.44, P.45, D.72, Y.85, G.137, I.138, G.139, H.143, A.145, F.146, R.172, K.208 Ligands: SO4.18 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:T.41, D:S.43, D:T.44, D:D.72, D:Y.85, D:Y.85, D:G.137, D:H.143, D:A.145, D:A.145, D:R.172 Water bridges: D:T.41, D:T.41, D:T.41, D:S.43, D:T.44, D:T.44, D:T.44, D:G.137, D:N.170, D:N.170, D:R.172, D:K.208 Salt bridges: D:K.208 AGP.22: 14 residues within 4Å: Chain E: T.41, G.42, S.43, T.44, M.71, D.72, Y.85, G.137, I.138, H.143, A.145, F.146, K.208 Ligands: SO4.21 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:T.41, E:T.41, E:T.41, E:S.43, E:T.44, E:T.44, E:D.72, E:H.143, E:A.145, E:A.145 Water bridges: E:M.71, E:G.137, E:K.208, E:K.208 Salt bridges: E:K.208 AGP.25: 16 residues within 4Å: Chain F: P.40, T.41, G.42, S.43, T.44, P.45, M.71, D.72, G.137, I.138, H.143, A.145, F.146, R.172, K.208 Ligands: SO4.24 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:T.41, F:T.41, F:T.41, F:S.43, F:T.44, F:T.44, F:D.72, F:G.137, F:H.143, F:A.145, F:A.145, F:R.172, F:R.172 Water bridges: F:D.72, F:G.137, F:I.138, F:K.208, F:K.208, F:K.208 Salt bridges: F:K.208

Links

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Citation

Arreola, R. et al., Two mammalian glucosamine-6-phosphate deaminases: a structural and genetic study. Febs Lett. (2003)

Release Date

2003-09-23

Peptides

Glucosamine-6-phosphate isomerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glucosamine-6-phosphate isomerase