SMTL ID : 2f3r.1

Crystal Structure Of E.coli Guanylate Kinase In Complex With Ap5G

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x G5P: P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE(Non-covalent)

G5P.1: 30 residues within 4Å: Chain A: S.13, G.14, A.15, G.16, K.17, S.18, S.19, 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, R.133, R.134, L.135, G.137 Chain E: L.30, Y.31, Q.34, T.95, V.97 28 PLIP interactions: 2 interactions with chain E, 26 interactions with chain A Hydrogen bonds: E:Q.34, E:T.95, A:S.13, A:G.14, A:A.15, A:G.16, A:G.16, A:K.17, A:K.17, A:S.18, A:S.18, A:S.18, A:S.19, A:S.38, A:Y.54, A:T.84, A:D.102, A:D.104, A:G.107, A:G.137 Salt bridges: A:K.17, A:K.17, A:K.17, A:R.42, A:R.45, A:R.45, A:E.73, A:D.104 G5P.2: 28 residues within 4Å: Chain B: S.13, G.14, A.15, G.16, K.17, S.18, S.19, 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, R.134, G.137 Chain D: Y.31, Q.34, V.92, T.95, V.97 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.14, B:A.15, B:G.16, B:G.16, B:K.17, B:S.18, B:S.18, B:S.19, B:S.38, B:Y.54, B:Y.82, B:D.102, B:D.102, B:D.104, B:G.107, D:Y.31, D:Q.34 Salt bridges: B:K.17, B:K.17, B:K.17, B:R.42, B:R.45, B:R.45, B:E.73, B:D.104 G5P.3: 30 residues within 4Å: Chain A: L.30, Y.31, Q.34, T.95, V.97 Chain C: S.13, G.14, A.15, G.16, K.17, S.18, S.19, 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, R.133, R.134, L.135, G.137 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.13, C:G.14, C:A.15, C:G.16, C:G.16, C:K.17, C:K.17, C:S.18, C:S.18, C:S.18, C:S.19, C:S.38, C:Y.54, C:T.84, C:D.102, C:D.104, C:G.107, C:G.137, A:Q.34, A:T.95 Salt bridges: C:K.17, C:K.17, C:K.17, C:R.42, C:R.45, C:R.45, C:E.73, C:D.104 G5P.4: 28 residues within 4Å: Chain D: S.13, G.14, A.15, G.16, K.17, S.18, S.19, 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, R.134, G.137 Chain F: Y.31, Q.34, V.92, T.95, V.97 25 PLIP interactions: 23 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:G.14, D:A.15, D:G.16, D:G.16, D:K.17, D:S.18, D:S.18, D:S.19, D:S.38, D:Y.54, D:Y.82, D:D.102, D:D.102, D:D.104, D:G.107, F:Y.31, F:Q.34 Salt bridges: D:K.17, D:K.17, D:K.17, D:R.42, D:R.45, D:R.45, D:E.73, D:D.104 G5P.5: 30 residues within 4Å: Chain C: L.30, Y.31, Q.34, T.95, V.97 Chain E: S.13, G.14, A.15, G.16, K.17, S.18, S.19, 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, R.133, R.134, L.135, G.137 28 PLIP interactions: 26 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:S.13, E:G.14, E:A.15, E:G.16, E:G.16, E:K.17, E:K.17, E:S.18, E:S.18, E:S.18, E:S.19, E:S.38, E:Y.54, E:T.84, E:D.102, E:D.104, E:G.107, E:G.137, C:Q.34, C:T.95 Salt bridges: E:K.17, E:K.17, E:K.17, E:R.42, E:R.45, E:R.45, E:E.73, E:D.104 G5P.6: 28 residues within 4Å: Chain B: Y.31, Q.34, V.92, T.95, V.97 Chain F: S.13, G.14, A.15, G.16, K.17, S.18, S.19, 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, R.134, G.137 25 PLIP interactions: 2 interactions with chain B, 23 interactions with chain F Hydrogen bonds: B:Y.31, B:Q.34, F:G.14, F:A.15, F:G.16, F:G.16, F:K.17, F:S.18, F:S.18, F:S.19, F:S.38, F:Y.54, F:Y.82, F:D.102, F:D.102, F:D.104, F:G.107 Salt bridges: F:K.17, F:K.17, F:K.17, F:R.42, F:R.45, F:R.45, F:E.73, F:D.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hible, G. et al., Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G. Biochimie (2006)

Release Date

2006-05-30

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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