SMTL ID : 1vkm.2 (2 other biounits)

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 4 residues within 4Å: Chain A: H.8, H.10 Chain B: E.216, E.218 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.216, B:E.218, A:H.8, A:H.10, H2O.7 MN.2: 2 residues within 4Å: Chain A: D.138 Chain B: E.172 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.138, H2O.1, H2O.1, H2O.1, H2O.7, H2O.7 MN.6: 4 residues within 4Å: Chain B: H.8, H.10 Chain C: E.216, E.218 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.216, C:E.218, B:H.8, B:H.10, H2O.12 MN.7: 2 residues within 4Å: Chain B: D.138 Chain C: E.172 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.138, H2O.7, H2O.7, H2O.7, H2O.13, H2O.13 MN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.13: 4 residues within 4Å: Chain A: E.216, E.218 Chain C: H.8, H.10 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.8, C:H.10, A:E.216, A:E.218, H2O.1 MN.14: 1 residues within 4Å: Chain C: D.138 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.138, H2O.1, H2O.1, H2O.12, H2O.12, H2O.12 MN.15: 2 residues within 4Å: Chain C: E.241, E.245 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.241, C:E.245, H2O.17, H2O.18, H2O.18

3 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)

UNL.3: 13 residues within 4Å: Chain A: E.29, T.31, K.89, T.108, V.109, T.126, G.128, G.130, S.140, D.142, K.159, K.254, T.257 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.109, A:G.128, A:G.130, A:S.140, A:D.142, A:K.159 Water bridges: A:K.89, A:K.89, A:S.110, A:G.128, A:Q.141, A:Q.141, A:Q.141, A:Q.141, A:D.142, A:G.253, A:T.257, A:T.257, B:E.172 Salt bridges: A:K.89 UNL.9: 12 residues within 4Å: Chain B: E.29, T.31, K.89, T.108, V.109, T.126, G.128, G.130, S.140, D.142, K.159, T.257 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:V.109, B:G.128, B:G.130, B:S.140, B:D.142, B:K.159 Water bridges: B:K.89, B:K.89, B:S.110, B:G.127, B:Q.141, B:Q.141, B:Q.141, B:D.142, B:G.253, B:T.257, B:T.257, B:T.257, C:E.172, C:E.172 Salt bridges: B:K.89 UNL.16: 13 residues within 4Å: Chain C: E.29, T.31, K.89, T.108, V.109, T.126, G.128, G.130, S.140, D.142, K.159, K.254, T.257 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:V.109, C:T.126, C:G.128, C:G.130, C:S.140, C:D.142, C:K.159 Water bridges: C:K.89, C:G.127, C:Q.141, C:Q.141, C:Q.141, C:D.142, C:D.142, C:T.257, C:T.257, A:E.172, A:E.172, A:E.172 Salt bridges: C:K.89

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

EDO.4: 6 residues within 4Å: Chain A: R.93, E.94, I.97 Chain B: P.177, L.178, P.199 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.178, A:R.93 EDO.5: 6 residues within 4Å: Chain A: D.88, V.90, E.94, I.97, V.98 Chain B: R.197 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.88, B:R.197 EDO.10: 4 residues within 4Å: Chain B: T.144, S.147, L.174 Chain C: L.174 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: R.136, V.139, M.170 Chain B: M.170, T.173 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: L.162, D.163, V.164, E.165 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:V.164, B:E.165 Water bridges: B:L.162, B:L.162, B:D.163, B:E.165, B:E.165, B:E.165, B:E.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levin, I. et al., Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold. Proteins (2005)

Release Date

2004-06-29

Peptides

conserved hypothetical protein TM1464: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

conserved hypothetical protein TM1464

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