SMTL ID : 5hj5.1 (5 other biounits)

Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE-6-PHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x F6R: FRUCTOSE -6-PHOSPHATE(Non-covalent)

F6R.1: 14 residues within 4Å: Chain A: P.40, T.41, G.42, G.43, T.44, M.71, D.72, G.137, V.138, G.139, H.143, A.145, R.172, K.208 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.41, A:T.41, A:G.43, A:T.44, A:T.44, A:G.137, A:H.143, A:A.145 Water bridges: A:D.72, A:V.138, A:A.145, A:A.145, A:N.170, A:R.172, A:R.172, A:R.172 Salt bridges: A:R.172, A:K.208 F6R.6: 14 residues within 4Å: Chain B: P.40, T.41, G.42, G.43, T.44, M.71, D.72, G.137, V.138, G.139, H.143, A.145, R.172, K.208 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.41, B:T.41, B:G.43, B:T.44, B:T.44, B:G.137, B:H.143, B:A.145 Water bridges: B:D.72, B:V.138, B:A.145, B:A.145, B:N.170, B:R.172, B:R.172, B:R.172 Salt bridges: B:R.172, B:K.208 F6R.11: 14 residues within 4Å: Chain C: P.40, T.41, G.42, G.43, T.44, M.71, D.72, G.137, V.138, G.139, H.143, A.145, R.172, K.208 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:T.41, C:T.41, C:G.43, C:T.44, C:T.44, C:G.137, C:H.143, C:A.145 Water bridges: C:D.72, C:V.138, C:A.145, C:A.145, C:N.170, C:R.172, C:R.172, C:R.172 Salt bridges: C:R.172, C:K.208

3 x BG6: 6-O-phosphono-beta-D-glucopyranose(Non-covalent)

BG6.2: 8 residues within 4Å: Chain A: M.1, R.2 Chain C: S.151, S.152, R.158, I.159, K.160, T.161 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.151, C:S.152, C:T.161, C:T.161, C:T.161, C:T.161, A:M.1, A:M.1 Water bridges: C:S.152, C:K.160, C:K.160 Salt bridges: C:R.158, C:K.160, C:K.160 BG6.7: 8 residues within 4Å: Chain A: S.151, S.152, R.158, I.159, K.160, T.161 Chain B: M.1, R.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.151, A:S.152, A:T.161, A:T.161, A:T.161, A:T.161, B:M.1, B:M.1 Water bridges: A:S.152, A:K.160, A:K.160 Salt bridges: A:R.158, A:K.160, A:K.160 BG6.12: 8 residues within 4Å: Chain B: S.151, S.152, R.158, I.159, K.160, T.161 Chain C: M.1, R.2 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.151, B:S.152, B:T.161, B:T.161, B:T.161, B:T.161, C:M.1, C:M.1 Water bridges: B:S.152, B:K.160, B:K.160 Salt bridges: B:R.158, B:K.160, B:K.160

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Y.90, F.94, N.95, I.97, I.99, E.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:E.101, A:E.101 GOL.4: 6 residues within 4Å: Chain A: R.86, Y.90, E.101, I.104, N.105, L.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.86, A:Y.90, A:L.106, A:L.106 Water bridges: A:R.86, A:R.120 GOL.5: 7 residues within 4Å: Chain A: K.130, L.194, D.195, A.196, Q.197, H.232, P.233 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.130 Water bridges: A:Q.197, C:S.154, C:S.154 GOL.8: 6 residues within 4Å: Chain B: Y.90, F.94, N.95, I.97, I.99, E.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.95, B:E.101, B:E.101 GOL.9: 6 residues within 4Å: Chain B: R.86, Y.90, E.101, I.104, N.105, L.106 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.86, B:Y.90, B:L.106, B:L.106 Water bridges: B:R.86, B:R.120 GOL.10: 7 residues within 4Å: Chain B: K.130, L.194, D.195, A.196, Q.197, H.232, P.233 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:S.154, A:S.154, B:Q.197 Hydrogen bonds: B:K.130 GOL.13: 6 residues within 4Å: Chain C: Y.90, F.94, N.95, I.97, I.99, E.101 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.95, C:E.101, C:E.101 GOL.14: 6 residues within 4Å: Chain C: R.86, Y.90, E.101, I.104, N.105, L.106 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.86, C:Y.90, C:L.106, C:L.106 Water bridges: C:R.86, C:R.120 GOL.15: 7 residues within 4Å: Chain C: K.130, L.194, D.195, A.196, Q.197, H.232, P.233 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.130 Water bridges: C:Q.197, B:S.154, B:S.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE -6-PHOSPHATE. To Be Published

Release Date

2016-02-03

Peptides

Glucosamine-6-phosphate deaminase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Glucosamine-6-phosphate deaminase

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