SMTL ID : 1c9k.1

THE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADENOSYLCOBINAMIDE PHOSPHATE GUALYLYLTRANSFERASE (COBU) COMPLEXED WITH GMP: EVIDENCE FOR A SUBSTRATE INDUCED TRANSFERASE ACTIVE SITE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: G.7, A.8, R.9, S.10, G.11, K.12, S.13 Chain C: Q.159 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.7, A:R.9, A:S.10, A:G.11, A:K.12, A:S.13, A:S.13, C:Q.159 Water bridges: A:R.9, A:R.9, A:K.12 Salt bridges: A:R.9, A:K.12 PO4.3: 6 residues within 4Å: Chain B: G.7, R.9, S.10, G.11, K.12, S.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.9, B:S.10, B:G.11, B:K.12, B:S.13 Salt bridges: B:R.9, B:K.12

3 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.2: 15 residues within 4Å: Chain A: Y.28, A.30, T.31, S.32, I.34, R.42, I.43, H.46, K.47, R.50, T.56, E.58, E.80, C.81, T.84 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.28, A:T.31, A:S.32, A:S.32, A:S.32, A:R.42, A:K.47, A:R.50, A:R.50, A:E.58, A:E.80, A:C.81, A:T.84 Water bridges: A:I.34 Salt bridges: A:E.58 5GP.4: 13 residues within 4Å: Chain B: S.13, Y.28, A.30, T.31, S.32, I.43, H.46, K.47, R.50, T.56, E.58, E.80, C.81 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.13, B:T.31, B:S.32, B:S.32, B:S.32, B:R.50, B:R.50, B:E.80 Water bridges: B:S.13 Salt bridges: B:E.58 5GP.7: 11 residues within 4Å: Chain C: Y.28, A.30, T.31, S.32, I.34, K.47, R.50, T.56, E.80, C.81, T.84 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.32, C:S.32, C:S.32, C:R.50, C:R.50, C:E.80, C:C.81

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain C: S.13, E.80 Ligands: POP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.13

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.6: 8 residues within 4Å: Chain C: G.7, A.8, R.9, S.10, G.11, K.12, S.13 Ligands: MG.5 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.9, C:S.10, C:S.10, C:G.11, C:K.12, C:S.13, B:Q.159 Water bridges: C:R.9, C:R.14, C:N.134, C:N.134 Salt bridges: C:R.9, C:R.9, C:K.12, C:K.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, T.B. et al., Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site. Biochemistry (1999)

Release Date

1999-08-18

Peptides

ADENOSYLCOBINAMIDE KINASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

ADENOSYLCOBINAMIDE KINASE

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