SMTL ID : 4hx0.2 (1 other biounit)

Crystal structure of a putative nucleotidyltransferase (TM1012) from Thermotoga maritima at 1.87 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

6 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: M.6, I.7, H.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.7 Water bridges: A:H.1, A:T.125, A:H.126 NA.2: 6 residues within 4Å: Chain A: H.1, H.5, A.38, G.41, V.42, P.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.38 NA.3: 3 residues within 4Å: Chain A: N.28, N.117, K.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.117, A:N.117 NA.21: 3 residues within 4Å: Chain B: M.6, I.7, H.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.1, B:I.7 NA.22: 6 residues within 4Å: Chain B: H.1, H.5, A.38, G.41, V.42, P.43 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.42 NA.23: 3 residues within 4Å: Chain B: N.28, N.117, K.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.117, B:K.120

10 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 8 residues within 4Å: Chain A: T.32, M.98, I.101, L.145 Chain B: K.150, T.153, W.157 Ligands: MPD.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.150, B:T.153, B:W.157, A:I.101 MPD.5: 10 residues within 4Å: Chain A: T.32, Q.52, I.101, K.103, L.133, Y.137, E.138, A.141, Y.142 Ligands: MPD.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.133, A:Y.142 Hydrogen bonds: A:T.32, A:T.32 Water bridges: A:Q.52 MPD.6: 7 residues within 4Å: Chain A: Q.140, R.147 Chain B: S.34, F.37, V.42, V.44, Y.142 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.37, B:V.42, B:V.44, B:V.44, B:Y.142 Hydrogen bonds: B:S.34, A:Q.140 MPD.7: 4 residues within 4Å: Chain A: L.12, R.16, H.126, M.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.16 MPD.8: 3 residues within 4Å: Chain A: F.75, R.102, W.110 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.75, A:F.75 Hydrogen bonds: A:R.102, A:W.110 MPD.24: 8 residues within 4Å: Chain A: K.150, T.153, W.157 Chain B: T.32, M.98, I.101, L.145 Ligands: MPD.25 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.101, A:K.150, A:T.153, A:W.157 MPD.25: 10 residues within 4Å: Chain B: T.32, Q.52, I.101, K.103, L.133, Y.137, E.138, A.141, Y.142 Ligands: MPD.24 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.133, B:Y.142 Hydrogen bonds: B:T.32 Water bridges: B:Q.52 MPD.26: 7 residues within 4Å: Chain A: S.34, F.37, V.42, V.44, Y.142 Chain B: Q.140, R.147 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.37, A:V.42, A:V.44, A:V.44, A:Y.142 Hydrogen bonds: A:S.34, B:Q.140 MPD.27: 4 residues within 4Å: Chain B: L.12, R.16, H.126, M.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.16 MPD.28: 3 residues within 4Å: Chain B: F.75, R.102, W.110 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.75, B:F.75 Hydrogen bonds: B:R.102, B:W.110

24 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.9: 4 residues within 4Å: Chain A: K.17, R.21, F.68, D.91 Ligand excluded by PLIP BU1.10: 5 residues within 4Å: Chain A: S.77, T.78, E.79 Chain B: K.156, E.160 Ligand excluded by PLIP BU1.11: 7 residues within 4Å: Chain A: S.34, H.47, D.48, D.50, Y.142 Chain B: K.150 Ligands: BU1.37 Ligand excluded by PLIP BU1.12: 3 residues within 4Å: Chain A: L.105, E.111, D.112 Ligand excluded by PLIP BU1.13: 2 residues within 4Å: Chain A: E.106, D.107 Ligand excluded by PLIP BU1.14: 6 residues within 4Å: Chain A: K.80, R.147, V.148, A.151, E.152, R.155 Ligand excluded by PLIP BU1.15: 8 residues within 4Å: Chain A: Y.19, L.22, K.23, E.25, V.27, W.29, F.122, K.129 Ligand excluded by PLIP BU1.16: 2 residues within 4Å: Chain A: E.106 Chain B: H.47 Ligand excluded by PLIP BU1.17: 6 residues within 4Å: Chain A: R.147, K.150, A.151, L.154, R.155 Ligands: BU1.31 Ligand excluded by PLIP BU1.18: 4 residues within 4Å: Chain A: Y.59, V.73, R.74, F.75 Ligand excluded by PLIP BU1.19: 4 residues within 4Å: Chain A: V.42, L.135, E.136, Y.139 Ligand excluded by PLIP BU1.20: 7 residues within 4Å: Chain A: H.5, M.6, I.7, R.8, Y.11, E.45, V.46 Ligand excluded by PLIP BU1.29: 4 residues within 4Å: Chain B: K.17, R.21, F.68, D.91 Ligand excluded by PLIP BU1.30: 5 residues within 4Å: Chain A: K.156, E.160 Chain B: S.77, T.78, E.79 Ligand excluded by PLIP BU1.31: 7 residues within 4Å: Chain A: K.150 Chain B: S.34, H.47, D.48, D.50, Y.142 Ligands: BU1.17 Ligand excluded by PLIP BU1.32: 3 residues within 4Å: Chain B: L.105, E.111, D.112 Ligand excluded by PLIP BU1.33: 2 residues within 4Å: Chain B: E.106, D.107 Ligand excluded by PLIP BU1.34: 6 residues within 4Å: Chain B: K.80, R.147, V.148, A.151, E.152, R.155 Ligand excluded by PLIP BU1.35: 8 residues within 4Å: Chain B: Y.19, L.22, K.23, E.25, V.27, W.29, F.122, K.129 Ligand excluded by PLIP BU1.36: 2 residues within 4Å: Chain A: H.47 Chain B: E.106 Ligand excluded by PLIP BU1.37: 6 residues within 4Å: Chain B: R.147, K.150, A.151, L.154, R.155 Ligands: BU1.11 Ligand excluded by PLIP BU1.38: 4 residues within 4Å: Chain B: Y.59, V.73, R.74, F.75 Ligand excluded by PLIP BU1.39: 4 residues within 4Å: Chain B: V.42, L.135, E.136, Y.139 Ligand excluded by PLIP BU1.40: 7 residues within 4Å: Chain B: H.5, M.6, I.7, R.8, Y.11, E.45, V.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boyko, K.M. et al., Crystal structure of putative nucleotidyltransferase with two MPD molecules in the active site. To be Published

Release Date

2013-09-11

Peptides

Putative nucleotidyltransferase TM1012: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative nucleotidyltransferase TM1012

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