SMTL ID : 2qeu.1

Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-hexamer

Ligands

14 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: V.99, D.100, E.133 Chain B: Y.38 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.133 Hydrophobic interactions: B:Y.38 ACT.2: 4 residues within 4Å: Chain A: E.81, P.82, I.83, G.84 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.82, A:I.83 Hydrogen bonds: A:E.81, A:I.83, A:G.84 ACT.3: 6 residues within 4Å: Chain A: I.78, R.79, Y.113 Chain E: Y.113 Ligands: GOL.7, GOL.14 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:Y.113 Hydrogen bonds: E:Y.113, E:Y.113 ACT.4: 6 residues within 4Å: Chain A: T.52, M.53, K.55, A.61, K.68 Chain E: E.104 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:K.55, A:A.61, E:E.104 Hydrogen bonds: A:K.55, E:E.104 Salt bridges: A:K.55, A:K.68 ACT.5: 6 residues within 4Å: Chain A: M.25, G.26, G.27, L.28, P.29, N.87 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.29, A:N.87 Water bridges: A:N.87 ACT.8: 6 residues within 4Å: Chain B: M.25, G.27, L.28, P.29, N.87, R.90 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.29 Water bridges: B:E.30, B:R.90 Salt bridges: B:R.90 ACT.11: 3 residues within 4Å: Chain C: V.99, D.100, E.133 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.100 ACT.15: 4 residues within 4Å: Chain D: V.99, D.100, E.133 Chain E: Y.38 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.133 Water bridges: D:D.100 Hydrophobic interactions: E:Y.38 ACT.16: 4 residues within 4Å: Chain D: E.81, P.82, I.83, G.84 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:P.82, D:I.83 Hydrogen bonds: D:I.83, D:G.84 ACT.17: 6 residues within 4Å: Chain B: Y.113 Chain D: I.78, R.79, Y.113 Ligands: GOL.21, GOL.28 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.113 Hydrogen bonds: B:Y.113 ACT.18: 6 residues within 4Å: Chain B: E.104 Chain D: T.52, M.53, K.55, A.61, K.68 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:K.55, D:A.61, B:E.104 Hydrogen bonds: D:T.52, D:K.55, B:E.104 Salt bridges: D:K.55, D:K.68 ACT.19: 6 residues within 4Å: Chain D: M.25, G.26, G.27, L.28, P.29, N.87 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:P.29, D:N.87 Water bridges: D:N.87 ACT.22: 6 residues within 4Å: Chain E: M.25, G.27, L.28, P.29, N.87, R.90 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:P.29 Water bridges: E:E.30, E:R.90 Salt bridges: E:R.90 ACT.25: 3 residues within 4Å: Chain F: V.99, D.100, E.133 1 PLIP interactions: 1 interactions with chain F Water bridges: F:D.100

6 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 11 residues within 4Å: Chain A: M.25, L.32, Y.46, R.50, D.76, E.81, G.84, H.88 Chain C: M.115, P.116 Chain E: I.111 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: A:D.76 Salt bridges: A:R.50, A:H.88, A:H.88 Hydrophobic interactions: E:I.111, C:P.116 CIT.9: 10 residues within 4Å: Chain A: M.115, P.116 Chain B: M.25, P.29, Y.46, R.50, D.76, H.88 Chain D: I.111, V.112 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.76, B:H.88 Salt bridges: B:R.50, B:H.88 Hydrophobic interactions: D:I.111 CIT.12: 9 residues within 4Å: Chain B: M.115, P.116 Chain C: Y.46, R.50, D.76, E.81, G.84, H.88 Chain F: I.111 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:D.76 Water bridges: C:E.81 Salt bridges: C:R.50, C:H.88, C:H.88 Hydrophobic interactions: F:I.111 CIT.20: 11 residues within 4Å: Chain B: I.111 Chain D: M.25, L.32, Y.46, R.50, D.76, E.81, G.84, H.88 Chain F: M.115, P.116 7 PLIP interactions: 1 interactions with chain F, 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: F:P.116, B:I.111 Hydrogen bonds: D:Y.46, D:D.76 Salt bridges: D:R.50, D:H.88, D:H.88 CIT.23: 10 residues within 4Å: Chain A: I.111, V.112 Chain D: M.115, P.116 Chain E: M.25, P.29, Y.46, R.50, D.76, H.88 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Y.46, E:D.76, E:H.88 Salt bridges: E:R.50, E:H.88 Hydrophobic interactions: A:I.111 CIT.26: 9 residues within 4Å: Chain C: I.111 Chain E: M.115, P.116 Chain F: Y.46, R.50, D.76, E.81, G.84, H.88 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:Y.46, F:D.76 Water bridges: F:E.81 Salt bridges: F:R.50, F:H.88, F:H.88 Hydrophobic interactions: C:I.111

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: Y.113 Chain C: Y.113 Chain E: I.78, R.79, Y.113 Chain F: R.79 Ligands: ACT.3, GOL.14, GOL.28 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain F Water bridges: E:R.79, F:R.79 Hydrogen bonds: A:Y.113 GOL.10: 4 residues within 4Å: Chain B: V.99, D.100, E.133 Chain C: Y.38 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.100, B:E.133 Water bridges: B:D.100, B:D.100 GOL.13: 7 residues within 4Å: Chain C: M.25, G.26, G.27, L.28, P.29, N.87, R.90 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.28, C:R.90 Water bridges: C:G.26, C:N.87 GOL.14: 10 residues within 4Å: Chain A: R.79 Chain C: I.78, R.79, Y.113 Chain E: Y.113 Chain F: Y.113 Ligands: ACT.3, GOL.7, GOL.21, GOL.28 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain F Water bridges: A:R.79 Hydrogen bonds: C:I.78, F:Y.113 GOL.21: 9 residues within 4Å: Chain B: I.78, R.79, Y.113 Chain C: R.79 Chain D: Y.113 Chain F: Y.113 Ligands: GOL.14, ACT.17, GOL.28 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:R.79, B:R.79 GOL.24: 4 residues within 4Å: Chain E: V.99, D.100, E.133 Chain F: Y.38 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.100, E:E.133 Water bridges: E:D.100, E:D.100 GOL.27: 7 residues within 4Å: Chain F: M.25, G.26, G.27, L.28, P.29, N.87, R.90 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:L.28, F:R.90 Water bridges: F:G.26, F:N.87 GOL.28: 10 residues within 4Å: Chain B: Y.113 Chain C: Y.113 Chain D: R.79 Chain F: I.78, R.79, Y.113 Ligands: GOL.7, GOL.14, ACT.17, GOL.21 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:I.78 Water bridges: D:R.79

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution. To be published

Release Date

2007-07-17

Peptides

Putative carboxymuconolactone decarboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Putative carboxymuconolactone decarboxylase