SMTL ID : 3r33.1

Evidence for dynamic motion in proteins as a mechanism for ligand dissociation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x 6ME: (6S)-6-methyl-5,6,7,8-tetrahydroquinazoline-2,4-diamine(Non-covalent)

6ME.1: 11 residues within 4Å: Chain A: I.5, A.6, A.7, D.27, L.28, F.31, I.50, I.94, Y.100, T.113 Ligands: NDP.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.28, A:F.31, A:F.31, A:I.50 Hydrogen bonds: A:I.5, A:A.6, A:T.113 Water bridges: A:A.6 Salt bridges: A:D.27 pi-Stacking: A:F.31

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 30 residues within 4Å: Chain A: A.6, A.7, I.14, G.15, M.16, N.18, A.19, M.20, W.22, G.43, R.44, H.45, T.46, L.62, S.63, S.64, K.76, S.77, I.94, G.95, G.96, G.97, R.98, V.99, Y.100, Q.102, T.123 Ligands: 6ME.1, CA.5, CA.7 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.46 Hydrogen bonds: A:A.7, A:A.7, A:N.18, A:N.18, A:R.44, A:H.45, A:H.45, A:T.46, A:T.46, A:S.64, A:G.96, A:G.97, A:R.98, A:R.98, A:R.98, A:V.99, A:Y.100, A:Q.102, A:Q.102, A:T.123 Water bridges: A:H.45, A:R.98 Salt bridges: A:R.44

17 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 2 residues within 4Å: Chain A: V.10, D.116 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.116, H2O.5 CA.5: 3 residues within 4Å: Chain A: R.44, Q.65 Ligands: NDP.2 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain A: R.52, P.53, R.71 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain A: N.18, M.20, S.49 Ligands: NDP.2 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain A: E.134, E.157, R.159 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.134, H2O.3 CA.9: 1 residues within 4Å: Chain A: E.17 No protein-ligand interaction detected (PLIP) CA.10: 4 residues within 4Å: Chain A: D.116, H.149 Ligands: CL.4, CL.19 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.116, A:H.149 CA.11: 4 residues within 4Å: Chain A: I.82, C.85, G.86, I.91 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.82, A:G.86 CA.12: 1 residues within 4Å: Chain A: E.101 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.101, H2O.3 CA.13: 2 residues within 4Å: Chain A: A.19, M.20 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain A: F.140, C.152 No protein-ligand interaction detected (PLIP) CA.15: 1 residues within 4Å: Chain A: D.11 No protein-ligand interaction detected (PLIP) CA.16: 1 residues within 4Å: Chain A: D.131 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, H2O.6 CA.17: 3 residues within 4Å: Chain A: R.12, D.127, Y.128 No protein-ligand interaction detected (PLIP) CA.20: 1 residues within 4Å: Chain A: D.122 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.122, H2O.4, H2O.5, H2O.6 CA.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.22: 4 residues within 4Å: Chain A: I.50, R.52, P.53, L.54 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.52, H2O.5, H2O.7

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: D.116, H.149, S.150 Ligands: CA.10, CL.19 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: K.32, P.55, R.57 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: D.116 Ligands: CL.4, CA.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carroll, M.J. et al., Evidence for dynamics in proteins as a mechanism for ligand dissociation. Nat.Chem.Biol. (2012)

Release Date

2012-01-25

Peptides

Dihydrofolate reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydrofolate reductase

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