SMTL ID : 3l21.1 (2 other biounits)

The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C) from Mycobacterium Tuberculosis - DHDPS-A204R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: Y.94 Chain B: T.93, Y.94, H.98 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Water bridges: B:P.63, B:P.63, B:K.70, B:K.70, B:T.93, B:Y.94, B:H.98 Salt bridges: B:H.98 Hydrogen bonds: A:Y.94 SO4.2: 3 residues within 4Å: Chain A: L.204, R.208, R.242 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.208, A:R.208, A:R.242, A:R.242, A:N.245 Salt bridges: A:R.208, A:R.242 SO4.3: 2 residues within 4Å: Chain A: S.28, G.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.29, A:D.30 SO4.12: 5 residues within 4Å: Chain A: L.258, G.259 Chain B: K.123, P.125 Ligands: ACT.18 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:K.123, B:P.124, A:S.256, A:G.259 SO4.13: 6 residues within 4Å: Chain A: K.123 Chain B: R.152, M.255, G.259, G.260 Ligands: ACT.19 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.260 Water bridges: B:R.152, B:R.152, B:R.152, B:V.261, A:K.123 Salt bridges: B:R.152, A:K.123 SO4.14: 2 residues within 4Å: Chain B: R.86, H.112 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.86 Salt bridges: B:R.86, B:H.112

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: D.180, L.181, H.182, S.183 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.182, A:S.183, A:S.183 Water bridges: A:K.178, A:D.180, A:L.181, A:L.181 GOL.5: 4 residues within 4Å: Chain A: L.78, G.82, D.83, H.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.83 Water bridges: A:L.78, A:G.82, A:R.86 GOL.9: 3 residues within 4Å: Chain A: P.150, P.156, K.178 No protein-ligand interaction detected (PLIP) GOL.10: 12 residues within 4Å: Chain A: S.56, G.57, T.58, S.62, G.90, A.91, G.92, L.115, V.116, V.117, Y.147 Chain B: Y.121 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.58, A:S.62, A:A.91, A:G.92, A:L.115, A:V.117, B:Y.121 Water bridges: A:S.62, A:Y.120 GOL.15: 5 residues within 4Å: Chain B: A.179, D.180, L.181, H.182, S.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.181, B:H.182, B:S.183 GOL.16: 2 residues within 4Å: Chain B: R.101 Ligands: GOL.20 No protein-ligand interaction detected (PLIP) GOL.17: 5 residues within 4Å: Chain B: S.32, L.33, E.69, E.72, R.279 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.33, B:E.72, B:R.279 GOL.20: 4 residues within 4Å: Chain B: D.67, I.71, R.101 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.67, B:R.101 Water bridges: B:A.105 GOL.23: 2 residues within 4Å: Chain B: A.108, E.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.109 Water bridges: B:E.109 GOL.25: 11 residues within 4Å: Chain A: Y.121 Chain B: S.56, G.57, T.58, S.62, G.90, A.91, G.92, L.115, V.116, V.117 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.62, B:S.62, B:A.91, B:G.92, B:L.115, B:V.117, A:Y.121

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain A: A.14, R.15, R.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.14 Water bridges: A:R.86 Salt bridges: A:R.86 ACT.7: 1 residues within 4Å: Chain A: R.304 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.304 Salt bridges: A:R.304 ACT.8: 3 residues within 4Å: Chain A: D.291, A.294, R.298 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.294 Water bridges: A:A.295 Salt bridges: A:R.298 ACT.18: 3 residues within 4Å: Chain B: P.125, Q.126 Ligands: SO4.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.126 Water bridges: B:Q.126, B:R.127 ACT.19: 5 residues within 4Å: Chain B: Y.147, I.149, R.152, K.175 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.260 Salt bridges: B:R.152 ACT.21: 2 residues within 4Å: Chain B: R.15 Ligands: ACT.22 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.15 ACT.22: 5 residues within 4Å: Chain B: F.10, P.143, P.169, N.170 Ligands: ACT.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.10 Hydrogen bonds: B:R.15

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.11: 2 residues within 4Å: Chain A: R.40, H.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.44

1 x PYR: PYRUVIC ACID(Non-covalent)

PYR.24: 5 residues within 4Å: Chain B: A.211, T.212, L.230, F.233, G.234 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.230 Water bridges: B:G.210, B:A.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, G.L. et al., A dimeric mutant of DHDPS from Mycobacterium tuberculosis. To be Published

Release Date

2010-12-15

Peptides

Dihydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrodipicolinate synthase

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