SMTL ID : 2rk2.1

DHFR R-67 complexed with NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 19 residues within 4Å: Chain A: K.16, A.20, Q.51, I.52, Y.53 Chain B: K.16, S.18, G.19, A.20, L.34, P.54, A.56, A.57 Chain D: G.48, S.49, V.50 Ligands: NAP.5, NAP.9, NAP.13 12 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:Q.51 Hydrogen bonds: A:A.20, A:Q.51, A:I.52, A:Y.53, D:V.50, B:A.20 Salt bridges: A:K.16, B:K.16 Water bridges: D:V.50, D:Q.51, B:K.16 NAP.5: 19 residues within 4Å: Chain A: K.16, S.18, G.19, A.20, L.34, P.54, A.56, A.57 Chain B: K.16, A.20, Q.51, I.52, Y.53 Chain C: G.48, S.49, V.50 Ligands: NAP.1, NAP.9, NAP.13 14 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:Q.51 Hydrogen bonds: B:A.20, B:Q.51, B:I.52, B:Y.53, A:A.20, A:T.35, C:V.50 Salt bridges: B:K.16, A:K.16 Water bridges: A:K.16, A:Y.30, C:V.50, C:Q.51 NAP.9: 19 residues within 4Å: Chain B: G.48, S.49, V.50 Chain C: K.16, A.20, Q.51, I.52, Y.53 Chain D: K.16, S.18, G.19, A.20, L.34, P.54, A.56, A.57 Ligands: NAP.1, NAP.5, NAP.13 12 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: C:Q.51 Hydrogen bonds: C:A.20, C:Q.51, C:I.52, C:Y.53, B:V.50, D:A.20 Salt bridges: C:K.16, D:K.16 Water bridges: B:V.50, B:Q.51, D:K.16 NAP.13: 19 residues within 4Å: Chain A: G.48, S.49, V.50 Chain C: K.16, S.18, G.19, A.20, L.34, P.54, A.56, A.57 Chain D: K.16, A.20, Q.51, I.52, Y.53 Ligands: NAP.1, NAP.5, NAP.9 14 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: D:Q.51 Hydrogen bonds: D:A.20, D:Q.51, D:I.52, D:Y.53, C:A.20, C:T.35, A:V.50 Salt bridges: D:K.16, C:K.16 Water bridges: C:K.16, C:Y.30, A:V.50, A:Q.51

12 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 2 residues within 4Å: Chain A: A.6, G.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.6 MRD.3: 2 residues within 4Å: Chain A: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.4: 5 residues within 4Å: Chain A: F.8, G.9, M.10, W.29, Y.39 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.29, A:Y.39 Water bridges: A:M.10 MRD.6: 2 residues within 4Å: Chain B: A.6, G.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.6 MRD.7: 2 residues within 4Å: Chain B: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.8: 5 residues within 4Å: Chain B: F.8, G.9, M.10, W.29, Y.39 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.29, B:Y.39 Water bridges: B:M.10 MRD.10: 2 residues within 4Å: Chain C: A.6, G.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.6 MRD.11: 2 residues within 4Å: Chain C: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.12: 5 residues within 4Å: Chain C: F.8, G.9, M.10, W.29, Y.39 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.29, C:Y.39 Water bridges: C:M.10 MRD.14: 2 residues within 4Å: Chain D: A.6, G.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.6 MRD.15: 2 residues within 4Å: Chain D: N.33, L.34 No protein-ligand interaction detected (PLIP) MRD.16: 5 residues within 4Å: Chain D: F.8, G.9, M.10, W.29, Y.39 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.29, D:Y.39 Water bridges: D:M.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krahn, J.M. et al., Crystal structure of a type II dihydrofolate reductase catalytic ternary complex. Biochemistry (2007)

Release Date

2008-06-03

Peptides

Dihydrofolate reductase type 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Dihydrofolate reductase type 2

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