SMTL ID : 9kce.2 (1 other biounit)

Crystal Structure of the ATP analog-bound closed state of Thermotoga maritima MutS2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 24 residues within 4Å: Chain A: I.298, R.302, V.303, V.304, I.306, P.322, N.323, M.324, G.325, G.326, K.327, T.328, V.329, E.402, Y.465 Chain B: Q.369, S.370, I.371, S.374, L.375, S.376, T.377, F.378 Ligands: MG.2 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.302, A:V.304, A:V.304, A:N.323, A:M.324, A:G.325, A:G.326, A:K.327, A:K.327, A:K.327, A:K.327, A:T.328, A:V.329, A:E.402, A:E.402, A:Y.465, B:Q.369, B:I.371, B:L.375, B:S.376, B:T.377, B:F.378 pi-Stacking: A:Y.465, A:Y.465 ANP.7: 23 residues within 4Å: Chain A: Q.369, I.371, S.374, S.376, T.377, F.378, G.406 Chain B: I.298, R.302, V.303, V.304, I.306, P.322, N.323, M.324, G.325, G.326, K.327, T.328, V.329, E.402, Y.465 Ligands: MG.3 22 PLIP interactions: 6 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:Q.369, A:I.371, A:S.376, A:T.377, A:T.377, A:F.378, B:R.302, B:V.304, B:V.304, B:N.323, B:M.324, B:G.325, B:G.326, B:K.327, B:K.327, B:K.327, B:T.328, B:T.328, B:V.329, B:E.402 pi-Stacking: B:Y.465, B:Y.465

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.328, D.401 Chain B: Q.369, T.377 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.328 MG.3: 6 residues within 4Å: Chain A: Q.369, T.377 Chain B: T.328, D.401, E.402 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.328

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

SO4.4: 4 residues within 4Å: Chain A: G.474, S.475, H.476 Chain B: E.411 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.411, A:H.476 Salt bridges: A:H.476 SO4.5: 5 residues within 4Å: Chain A: K.17, D.23, R.26, K.27, D.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.30 Water bridges: A:K.17 Salt bridges: A:K.17, A:K.27 SO4.6: 6 residues within 4Å: Chain A: R.181, D.182, H.202, H.203 Chain B: R.184, N.223 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.181, A:H.202, A:H.203, B:R.184 Hydrogen bonds: B:N.223 SO4.9: 9 residues within 4Å: Chain A: S.405, G.406, T.407, H.435, L.436 Chain B: S.405, G.406, H.435, L.436 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.405, B:G.406, A:S.405, A:G.406, A:T.407 Salt bridges: B:H.435, A:H.435 SO4.10: 3 residues within 4Å: Chain B: R.153, E.157, R.224 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.153, B:R.224

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: R.226 Chain B: H.202 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.226, A:R.226, B:H.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukui, K. et al., ATP binding controls the molecular function of bacterial MutS2 by mediating closure of the dimeric clamp structure. Structure (2025)

Release Date

2025-09-10

Peptides

Endonuclease MutS2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Endonuclease MutS2

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