SMTL ID : 1nhh.1

Crystal structure of N-terminal 40KD MutL protein (LN40) complex with ADPnP and one Rubidium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.35, K.81 Ligands: ANP.8 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: N.35, K.81 Ligands: ANP.16 No protein-ligand interaction detected (PLIP)

2 x RB: RUBIDIUM ION(Non-covalent)

RB.2: 6 residues within 4Å: Chain A: L.72, A.73, A.75, A.78, G.98 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.75 RB.10: 6 residues within 4Å: Chain B: L.72, A.73, A.75, A.78, G.98 Ligands: ANP.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.75

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: E.34, L.94, I.180, A.183, Y.259, G.262, R.263, M.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.34, A:E.34, A:G.262, A:M.264 EDO.4: 2 residues within 4Å: Chain A: W.231, Q.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.232 Water bridges: A:W.231 EDO.5: 3 residues within 4Å: Chain A: G.40, T.42, N.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.40, A:N.61 EDO.6: 5 residues within 4Å: Chain A: L.236, I.296, Q.300, Q.316, L.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.316 Water bridges: A:D.235 EDO.7: 3 residues within 4Å: Chain A: D.131, M.132, N.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.133 Water bridges: A:L.74, A:M.132, A:V.134 EDO.11: 8 residues within 4Å: Chain B: E.34, L.94, I.180, A.183, Y.259, G.262, R.263, M.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.34, B:E.34, B:G.262, B:M.264 EDO.12: 2 residues within 4Å: Chain B: W.231, Q.232 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.232 Water bridges: B:W.231 EDO.13: 3 residues within 4Å: Chain B: G.40, T.42, N.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.40, B:N.61 EDO.14: 5 residues within 4Å: Chain B: L.236, I.296, Q.300, Q.316, L.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.316 Water bridges: B:D.235 EDO.15: 3 residues within 4Å: Chain B: D.131, M.132, N.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.133 Water bridges: B:L.74, B:M.132, B:V.134

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.8: 23 residues within 4Å: Chain A: E.31, N.35, S.36, A.39, D.60, G.64, I.65, A.73, T.79, S.80, K.81, G.95, F.96, R.97, G.98, E.99, A.100, L.101, T.145, K.309 Chain B: I.5 Ligands: MG.1, RB.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:E.31, A:N.35, A:D.60, A:T.79, A:T.79, A:S.80, A:S.80, A:S.80, A:K.81, A:F.96, A:R.97, A:G.98, A:E.99, A:A.100, A:L.101, A:T.145, A:K.309, A:K.309 Water bridges: A:D.60, A:D.60, A:G.64, A:K.81, A:R.97 pi-Cation interactions: A:K.81 ANP.16: 23 residues within 4Å: Chain A: I.5 Chain B: E.31, N.35, S.36, A.39, D.60, G.64, I.65, A.73, T.79, S.80, K.81, G.95, F.96, R.97, G.98, E.99, A.100, L.101, T.145, K.309 Ligands: MG.9, RB.10 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:E.31, B:N.35, B:D.60, B:T.79, B:T.79, B:S.80, B:S.80, B:S.80, B:K.81, B:F.96, B:R.97, B:G.98, B:E.99, B:A.100, B:L.101, B:T.145, B:K.309, B:K.309 Water bridges: B:D.60, B:D.60, B:G.64, B:K.81, B:R.97 pi-Cation interactions: B:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, X. et al., Monovalent cation dependence and preference of GHKL ATPases and kinases. FEBS Lett. (2003)

Release Date

2003-06-10

Peptides

DNA mismatch repair protein mutL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA mismatch repair protein mutL

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