SMTL ID : 5hj5.5 (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 Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

6 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 F6R.16: 14 residues within 4Å: Chain D: 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 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:T.41, D:T.41, D:G.43, D:T.44, D:G.137, D:H.143, D:A.145 Water bridges: D:T.41, D:T.44, D:D.72, D:V.138, D:A.145, D:A.145, D:R.172, D:R.172, D:R.172, D:R.172 Salt bridges: D:R.172, D:K.208 F6R.19: 14 residues within 4Å: Chain E: 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 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:T.41, E:T.41, E:G.43, E:T.44, E:G.137, E:H.143, E:A.145 Water bridges: E:T.41, E:T.44, E:D.72, E:V.138, E:A.145, E:A.145, E:R.172, E:R.172, E:R.172, E:R.172 Salt bridges: E:R.172, E:K.208 F6R.22: 14 residues within 4Å: Chain F: 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 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:T.41, F:T.41, F:G.43, F:T.44, F:G.137, F:H.143, F:A.145 Water bridges: F:T.41, F:T.44, F:D.72, F:V.138, F:A.145, F:A.145, F:R.172, F:R.172, F:R.172, F:R.172 Salt bridges: F:R.172, F:K.208

6 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 BG6.17: 8 residues within 4Å: Chain D: M.1, R.2 Chain E: S.151, S.152, R.158, I.159, K.160, T.161 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain E Water bridges: D:M.1, D:P.233, E:S.152, E:R.158, E:K.160, E:T.161 Hydrogen bonds: E:S.152, E:T.161, E:T.161, E:T.161 Salt bridges: E:R.158, E:K.160, E:K.160 BG6.20: 8 residues within 4Å: Chain E: M.1, R.2 Chain F: S.151, S.152, R.158, I.159, K.160, T.161 13 PLIP interactions: 2 interactions with chain E, 11 interactions with chain F Water bridges: E:M.1, E:P.233, F:S.152, F:R.158, F:K.160, F:T.161 Hydrogen bonds: F:S.152, F:T.161, F:T.161, F:T.161 Salt bridges: F:R.158, F:K.160, F:K.160 BG6.23: 8 residues within 4Å: Chain D: S.151, S.152, R.158, I.159, K.160, T.161 Chain F: M.1, R.2 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain D Water bridges: F:M.1, F:P.233, D:S.152, D:R.158, D:K.160, D:T.161 Hydrogen bonds: D:S.152, D:T.161, D:T.161, D:T.161 Salt bridges: D:R.158, D:K.160, D:K.160

12 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 B, 2 interactions with chain A Hydrogen bonds: B:K.130 Water bridges: B:Q.197, A:S.154, A:S.154 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 GOL.18: 6 residues within 4Å: Chain D: I.24, N.25, Q.28, P.29, V.61, S.62 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.62 Water bridges: D:S.62, D:S.62 GOL.21: 6 residues within 4Å: Chain E: I.24, N.25, Q.28, P.29, V.61, S.62 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.62 Water bridges: E:S.62, E:S.62 GOL.24: 6 residues within 4Å: Chain F: I.24, N.25, Q.28, P.29, V.61, S.62 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.62 Water bridges: F:S.62, F:S.62

Links

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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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
C

E
C

F
C

Glucosamine-6-phosphate deaminase

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