SMTL ID : 1cf2.1

THREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS FERVIDUS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: S.139, C.140, N.141, R.167, H.193, H.194 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.139, A:S.139, A:N.141, A:N.141, A:T.142 Salt bridges: A:R.167, A:H.193, A:H.194 SO4.3: 7 residues within 4Å: Chain B: S.139, C.140, N.141, R.167, H.193, H.194, H.219 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.139, B:N.141, B:N.141 Salt bridges: B:R.167, B:H.193, B:H.194, B:H.219 SO4.5: 7 residues within 4Å: Chain C: S.139, C.140, N.141, R.167, H.193, H.194, H.219 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.139, C:N.141, C:N.141 Water bridges: C:R.168, C:H.193 Salt bridges: C:R.167, C:H.193, C:H.194, C:H.219 SO4.7: 6 residues within 4Å: Chain D: S.139, C.140, N.141, R.167, H.193, H.194 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.139, D:S.139, D:N.141, D:N.141 Salt bridges: D:R.167, D:H.193, D:H.194, D:H.219

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 22 residues within 4Å: Chain A: N.7, G.8, Y.9, G.10, T.11, V.12, K.33, T.34, R.35, A.53, C.85, T.86, P.87, E.88, I.90, Q.108, G.110, C.140, R.168, D.171, Q.300, I.304 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:V.12, A:I.304 Hydrogen bonds: A:Y.9, A:T.11, A:T.11, A:T.11, A:V.12, A:T.34, A:R.35, A:T.86, A:E.88, A:E.88, A:G.110, A:R.168, A:D.171 Water bridges: A:N.7, A:G.10, A:T.11, A:G.13, A:K.33, A:K.33, A:E.88, A:N.94, A:N.94, A:D.171, A:D.171, A:Q.174, A:Q.174, A:Q.174 Salt bridges: A:K.33 NAP.4: 23 residues within 4Å: Chain B: N.7, G.8, Y.9, G.10, T.11, V.12, K.33, T.34, R.35, A.53, C.85, T.86, P.87, E.88, I.90, Q.108, G.110, E.111, C.140, R.168, D.171, Q.300, I.304 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:V.12, B:I.304 Hydrogen bonds: B:Y.9, B:T.11, B:V.12, B:T.34, B:R.35, B:T.86, B:E.88, B:E.88, B:G.110, B:E.111, B:R.168, B:D.171 Water bridges: B:N.7, B:G.10, B:T.11, B:T.11, B:G.13, B:K.33, B:E.88, B:N.94, B:D.171 Salt bridges: B:K.33 NAP.6: 23 residues within 4Å: Chain C: N.7, G.8, Y.9, G.10, T.11, V.12, K.33, T.34, R.35, A.53, C.85, T.86, P.87, E.88, I.90, Q.108, G.110, C.140, R.168, D.171, Q.300, E.301, I.304 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:V.12, C:I.304 Hydrogen bonds: C:Y.9, C:T.11, C:T.11, C:T.11, C:V.12, C:T.34, C:R.35, C:T.86, C:E.88, C:G.110, C:R.168, C:D.171 Water bridges: C:N.7, C:G.10, C:T.11, C:G.13, C:K.33, C:K.33, C:K.33, C:E.88, C:N.94, C:N.94 Salt bridges: C:K.33 NAP.8: 24 residues within 4Å: Chain D: N.7, G.8, Y.9, G.10, T.11, V.12, S.32, K.33, T.34, R.35, A.53, C.85, T.86, P.87, E.88, I.90, Q.108, G.110, C.140, R.168, D.171, Q.300, E.301, I.304 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:V.12, D:I.304 Hydrogen bonds: D:Y.9, D:T.11, D:T.11, D:V.12, D:T.34, D:R.35, D:T.86, D:E.88, D:G.110, D:E.111, D:R.168, D:D.171 Water bridges: D:N.7, D:G.10, D:T.11, D:G.13, D:R.35, D:R.35, D:R.35, D:E.39, D:E.39, D:E.88, D:N.94, D:Q.174 Salt bridges: D:K.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Charron, C. et al., Crystallization and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus. Acta Crystallogr.,Sect.D (1999)

Release Date

2000-03-29

Peptides

PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
R

C
O

D
Q

PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)