SMTL ID : 2gq2.1

Mycobacterium tuberculosis ThyX-NADP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

15 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 4 residues within 4Å: Chain A: P.110, E.111, K.112, R.115 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: H.91 Chain D: R.87 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: P.120, G.121, V.206 Chain D: A.170 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: G.59, Y.60 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain C: R.87 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain B: R.87, R.172 Chain C: N.177 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain C: A.58, A.225 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain B: N.177 Chain C: R.87, Q.106, R.172 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain B: H.98 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain B: G.121 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: N.177 Chain D: R.87, M.175 Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain D: R.210, T.239, E.240 Ligands: GOL.31 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain D: P.120, G.121, V.206 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: R.97, H.98 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain A: D.205 Chain D: Q.166, Q.169 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: A.191 Ligands: NAP.19, NAP.28 No protein-ligand interaction detected (PLIP) K.11: 3 residues within 4Å: Chain B: A.191 Ligands: NAP.19, NAP.28 No protein-ligand interaction detected (PLIP) K.18: 3 residues within 4Å: Chain C: A.191 Ligands: NAP.6, NAP.12 No protein-ligand interaction detected (PLIP) K.27: 3 residues within 4Å: Chain D: A.191 Ligands: NAP.6, NAP.12 No protein-ligand interaction detected (PLIP)

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

NAP.6: 22 residues within 4Å: Chain A: S.100, Y.101, S.102, Q.103, S.105 Chain C: C.43, H.69, S.71, E.74, H.98, N.188, R.190, H.194 Chain D: R.95, H.96, R.97, H.98, H.194, R.199 Ligands: NAP.12, K.18, K.27 25 PLIP interactions: 3 interactions with chain A, 11 interactions with chain C, 11 interactions with chain D Hydrogen bonds: A:S.100, A:Q.103, C:S.71, C:H.98, C:N.188, D:R.97, D:R.97, D:H.98, D:H.194, D:R.199 Water bridges: A:Q.106, C:R.190, C:H.194 Salt bridges: C:R.190, C:R.190, C:H.194, D:H.96, D:H.96, D:R.97, D:R.97, D:H.194, D:H.194 pi-Stacking: C:H.98, C:H.98 pi-Cation interactions: C:H.69 NAP.12: 21 residues within 4Å: Chain B: S.100, Y.101, Q.103, S.105 Chain C: R.95, H.96, R.97, H.98, H.194, R.199 Chain D: Y.44, S.71, E.74, H.98, N.188, R.190, A.191, H.194 Ligands: NAP.6, K.18, K.27 23 PLIP interactions: 2 interactions with chain B, 11 interactions with chain C, 10 interactions with chain D Hydrogen bonds: B:S.100, B:Q.103, C:R.97, C:H.194, C:R.199, C:R.199, D:Y.44, D:S.71, D:N.188 Water bridges: C:R.97, D:H.194, D:H.194 Salt bridges: C:H.96, C:H.96, C:R.97, C:R.97, C:H.194, C:H.194, D:R.190, D:R.190, D:H.194 pi-Stacking: D:H.98, D:H.98 NAP.19: 22 residues within 4Å: Chain A: S.71, E.74, H.98, N.188, R.190, A.191, H.194 Chain B: R.95, H.96, R.97, H.98, H.194, R.199 Chain C: S.100, Y.101, S.102, Q.103, S.105 Ligands: K.5, PGE.7, K.11, NAP.28 26 PLIP interactions: 4 interactions with chain C, 11 interactions with chain B, 11 interactions with chain A Hydrogen bonds: C:S.100, C:S.105, B:R.97, B:R.97, B:H.194, B:R.199, A:S.71, A:N.188 Water bridges: C:Q.106, C:Q.106, A:H.98, A:R.190, A:R.190, A:H.194 Salt bridges: B:H.96, B:H.96, B:R.97, B:R.97, B:H.194, B:H.194, A:R.190, A:R.190, A:H.194 pi-Cation interactions: B:R.95 pi-Stacking: A:H.98, A:H.98 NAP.28: 21 residues within 4Å: Chain A: R.95, H.96, R.97, H.98, H.194, R.199 Chain B: C.43, S.71, E.74, H.98, N.188, R.190, A.191, H.194 Chain D: Y.101, S.102, Q.103, S.105 Ligands: K.5, K.11, NAP.19 25 PLIP interactions: 2 interactions with chain D, 10 interactions with chain B, 13 interactions with chain A Hydrogen bonds: D:S.100, D:S.105, B:S.71, B:N.188, A:H.96, A:R.97, A:R.97, A:H.194, A:R.199 Water bridges: B:R.190, B:R.190, B:H.194, A:R.95 Salt bridges: B:R.190, B:R.190, B:H.194, A:H.96, A:H.96, A:R.97, A:R.97, A:H.194, A:H.194 pi-Stacking: B:H.98, B:H.98 pi-Cation interactions: A:R.95

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 8 residues within 4Å: Chain A: Y.44, G.68, H.69, F.70, S.71, R.190 Chain C: S.105 Ligands: NAP.19 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.190, C:S.105

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: K.14, T.15, G.31, G.32, P.33, S.77, V.78, Y.189, V.222 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.15, A:G.32, A:S.77, A:S.77, A:V.222 GOL.13: 8 residues within 4Å: Chain B: K.14, T.15, G.31, G.32, P.33, V.78, Y.189, V.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.15, B:T.15, B:G.32 GOL.20: 8 residues within 4Å: Chain C: K.14, T.15, G.31, G.32, S.77, V.78, Y.189, V.222 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.15, C:T.15, C:T.15, C:G.32, C:S.77, C:Y.189 GOL.21: 4 residues within 4Å: Chain C: R.210, I.213, T.239, E.240 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.240, C:E.240 Water bridges: C:R.209, C:R.210, C:R.217 GOL.29: 9 residues within 4Å: Chain D: K.14, T.15, G.31, G.32, P.33, S.77, V.78, Y.189, V.222 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.15, D:T.15, D:G.32, D:S.77, D:S.77, D:Y.189, D:V.222 Water bridges: D:D.30 GOL.30: 7 residues within 4Å: Chain B: Y.81, R.182 Chain D: D.22, V.23, P.24, Q.45, W.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.81, B:Y.81, B:R.182 GOL.31: 6 residues within 4Å: Chain D: R.209, R.210, I.213, T.239, E.240 Ligands: IOD.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.209, D:T.239, D:E.240, D:E.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., NADP+ expels both the co-factor and a substrate analog from the Mycobacterium tuberculosis ThyX active site: opportunities for anti-bacterial drug design. J.Mol.Biol. (2006)

Release Date

2006-06-27

Peptides

Thymidylate synthase thyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thymidylate synthase thyX

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