SMTL ID : 2an9.1

Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-hexamer

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: S.38, Y.54, D.102 Ligands: GDP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.38, A:D.102, H2O.1, H2O.1 K.4: 3 residues within 4Å: Chain B: S.38, D.102 Ligands: GDP.5 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.38, B:D.102, H2O.4, H2O.4, H2O.5 K.7: 4 residues within 4Å: Chain C: S.38, Y.54, D.102 Ligands: GDP.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.38, C:D.102, H2O.8, H2O.8 K.10: 3 residues within 4Å: Chain D: S.38, D.102 Ligands: GDP.11 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.38, D:D.102, H2O.11, H2O.11, H2O.12 K.13: 4 residues within 4Å: Chain E: S.38, Y.54, D.102 Ligands: GDP.14 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.38, E:D.102, H2O.15, H2O.16 K.16: 3 residues within 4Å: Chain F: S.38, D.102 Ligands: GDP.17 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.38, F:D.102, H2O.18, H2O.18, H2O.19

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 16 residues within 4Å: Chain A: S.18, S.38, R.42, R.45, Y.54, E.73, A.75, V.77, Y.82, G.83, T.84, D.102, I.103, D.104, G.107 Ligands: K.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.17, A:K.17, A:S.18, A:S.18, A:S.18, A:S.38, A:Y.54, A:T.84, A:D.102, A:D.104, A:G.107 Water bridges: A:R.45, A:R.45 Salt bridges: A:K.17, A:R.42, A:R.45, A:R.45, A:E.73, A:D.104 GDP.5: 16 residues within 4Å: Chain B: S.13, K.17, S.38, R.42, R.45, Y.54, E.73, A.75, Y.82, G.83, T.84, D.102, I.103, D.104, G.107 Ligands: K.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.38, B:Y.54, B:Y.82, B:D.102, B:D.104, B:G.107 Water bridges: B:K.17, B:S.18, B:S.18, B:S.18, B:S.18 Salt bridges: B:K.17, B:R.42, B:R.45, B:R.45, B:E.73, B:D.104 GDP.8: 16 residues within 4Å: Chain C: S.18, S.38, R.42, R.45, Y.54, E.73, A.75, V.77, Y.82, G.83, T.84, D.102, I.103, D.104, G.107 Ligands: K.7 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:K.17, C:K.17, C:S.18, C:S.18, C:S.18, C:S.38, C:Y.54, C:T.84, C:D.102, C:D.104, C:G.107 Water bridges: C:R.45, C:R.45 Salt bridges: C:K.17, C:R.42, C:R.45, C:R.45, C:E.73, C:D.104 GDP.11: 16 residues within 4Å: Chain D: S.13, K.17, S.38, R.42, R.45, Y.54, E.73, A.75, Y.82, G.83, T.84, D.102, I.103, D.104, G.107 Ligands: K.10 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.38, D:Y.54, D:Y.82, D:D.102, D:D.104, D:G.107 Water bridges: D:K.17, D:S.18, D:S.18, D:S.18, D:S.18 Salt bridges: D:K.17, D:R.42, D:R.45, D:R.45, D:E.73, D:D.104 GDP.14: 16 residues within 4Å: Chain E: S.18, S.38, R.42, R.45, Y.54, E.73, A.75, V.77, Y.82, G.83, T.84, D.102, I.103, D.104, G.107 Ligands: K.13 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:K.17, E:K.17, E:S.18, E:S.18, E:S.18, E:S.38, E:Y.54, E:T.84, E:D.102, E:D.104, E:G.107 Water bridges: E:R.45, E:R.45 Salt bridges: E:K.17, E:R.42, E:R.45, E:R.45, E:E.73, E:D.104 GDP.17: 16 residues within 4Å: Chain F: S.13, K.17, S.38, R.42, R.45, Y.54, E.73, A.75, Y.82, G.83, T.84, D.102, I.103, D.104, G.107 Ligands: K.16 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:S.38, F:Y.54, F:Y.82, F:D.102, F:D.104, F:G.107 Water bridges: F:K.17, F:S.18, F:S.18, F:S.18, F:S.18 Salt bridges: F:K.17, F:R.42, F:R.45, F:R.45, F:E.73, F:D.104

6 x GMP: GUANOSINE(Non-covalent)

GMP.3: 10 residues within 4Å: Chain A: R.133, R.134, L.135, G.137, R.138 Chain E: L.30, Y.31, Q.34, T.95, V.97 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Y.31, E:Q.34, E:T.95, E:T.95, E:T.95, A:L.135 GMP.6: 10 residues within 4Å: Chain B: G.14, R.133, R.134, G.137, R.138 Chain D: L.30, Y.31, Q.34, T.95, V.97 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Y.31, D:Q.34, D:T.95, D:T.95, D:T.95 Water bridges: B:G.14, B:L.135 GMP.9: 10 residues within 4Å: Chain A: L.30, Y.31, Q.34, T.95, V.97 Chain C: R.133, R.134, L.135, G.137, R.138 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.31, A:Q.34, A:T.95, A:T.95, A:T.95, C:L.135 GMP.12: 10 residues within 4Å: Chain D: G.14, R.133, R.134, G.137, R.138 Chain F: L.30, Y.31, Q.34, T.95, V.97 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:Y.31, F:Q.34, F:T.95, F:T.95, F:T.95 Water bridges: D:G.14, D:L.135 GMP.15: 10 residues within 4Å: Chain C: L.30, Y.31, Q.34, T.95, V.97 Chain E: R.133, R.134, L.135, G.137, R.138 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain C Hydrogen bonds: E:L.135, C:Y.31, C:Q.34, C:T.95, C:T.95, C:T.95 GMP.18: 10 residues within 4Å: Chain B: L.30, Y.31, Q.34, T.95, V.97 Chain F: G.14, R.133, R.134, G.137, R.138 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:Y.31, B:Q.34, B:T.95, B:T.95, B:T.95 Water bridges: F:G.14, F:L.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hible, G. et al., Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. J.Mol.Biol. (2005)

Release Date

2005-08-30

Peptides

Guanylate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Guanylate kinase

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