SMTL ID : 4j7y.2 (1 other biounit)

Human LTC4 synthase in complex with product analogs - implications for enzyme catalysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-12-mer

Ligands

12 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 8 residues within 4Å: Chain A: H.5, H.7 Chain H: H.5, H.7 Chain J: H.5, H.7 Ligands: NI.22, NI.28 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain H, 1 interactions with chain A Metal complexes: J:H.7, H:H.7, A:H.7 NI.4: 8 residues within 4Å: Chain B: H.5, H.7 Chain E: H.5, H.7 Chain L: H.5, H.7 Ligands: NI.13, NI.34 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain L, 1 interactions with chain B Metal complexes: E:H.7, L:H.7, B:H.7 NI.7: 8 residues within 4Å: Chain C: H.5, H.7 Chain G: H.5, H.7 Chain K: H.5, H.7 Ligands: NI.19, NI.31 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C, 1 interactions with chain K Metal complexes: G:H.7, C:H.7, K:H.7 NI.10: 8 residues within 4Å: Chain D: H.5, H.7 Chain F: H.5, H.7 Chain I: H.5, H.7 Ligands: NI.16, NI.25 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 interactions with chain I Metal complexes: F:H.7, D:H.7, I:H.7 NI.13: 8 residues within 4Å: Chain B: H.5, H.7 Chain E: H.5, H.7 Chain L: H.5, H.7 Ligands: NI.4, NI.34 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain L, 1 interactions with chain B Metal complexes: E:H.7, L:H.7, B:H.7 NI.16: 8 residues within 4Å: Chain D: H.5, H.7 Chain F: H.5, H.7 Chain I: H.5, H.7 Ligands: NI.10, NI.25 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain D, 1 interactions with chain F Metal complexes: I:H.7, D:H.7, F:H.7 NI.19: 8 residues within 4Å: Chain C: H.5, H.7 Chain G: H.5, H.7 Chain K: H.5, H.7 Ligands: NI.7, NI.31 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain G, 1 interactions with chain C Metal complexes: K:H.7, G:H.7, C:H.7 NI.22: 8 residues within 4Å: Chain A: H.5, H.7 Chain H: H.5, H.7 Chain J: H.5, H.7 Ligands: NI.1, NI.28 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A, 1 interactions with chain H Metal complexes: J:H.7, A:H.7, H:H.7 NI.25: 8 residues within 4Å: Chain D: H.5, H.7 Chain F: H.5, H.7 Chain I: H.5, H.7 Ligands: NI.10, NI.16 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain D, 1 interactions with chain F Metal complexes: I:H.7, D:H.7, F:H.7 NI.28: 8 residues within 4Å: Chain A: H.5, H.7 Chain H: H.5, H.7 Chain J: H.5, H.7 Ligands: NI.1, NI.22 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A, 1 interactions with chain H Metal complexes: J:H.7, A:H.7, H:H.7 NI.31: 8 residues within 4Å: Chain C: H.5, H.7 Chain G: H.5, H.7 Chain K: H.5, H.7 Ligands: NI.7, NI.19 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C, 1 interactions with chain K Metal complexes: G:H.7, C:H.7, K:H.7 NI.34: 8 residues within 4Å: Chain B: H.5, H.7 Chain E: H.5, H.7 Chain L: H.5, H.7 Ligands: NI.4, NI.13 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain L, 1 interactions with chain E Metal complexes: B:H.7, L:H.7, E:H.7

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

SO4.2: 10 residues within 4Å: Chain A: R.54, R.105, S.106, A.107, Q.108 Chain B: R.54, S.106, A.107, Q.108 Ligands: SO4.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.107, A:Q.108, B:A.107, B:Q.108 Salt bridges: A:R.54 SO4.5: 10 residues within 4Å: Chain A: R.54, S.106, A.107, Q.108 Chain B: R.54, R.105, S.106, A.107, Q.108 Ligands: SO4.2 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.107, A:Q.108, B:A.107, B:Q.108 Salt bridges: B:R.54 SO4.8: 10 residues within 4Å: Chain C: R.54, R.105, S.106, A.107, Q.108 Chain D: R.54, S.106, A.107, Q.108 Ligands: SO4.11 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:A.107, D:Q.108, C:A.107, C:Q.108 Salt bridges: C:R.54 SO4.11: 10 residues within 4Å: Chain C: R.54, S.106, A.107, Q.108 Chain D: R.54, R.105, S.106, A.107, Q.108 Ligands: SO4.8 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:A.107, D:Q.108, C:A.107, C:Q.108 Salt bridges: D:R.54 SO4.14: 10 residues within 4Å: Chain E: R.54, R.105, S.106, A.107, Q.108 Chain F: R.54, S.106, A.107, Q.108 Ligands: SO4.17 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:A.107, E:Q.108, F:A.107, F:Q.108 Salt bridges: E:R.54 SO4.17: 10 residues within 4Å: Chain E: R.54, S.106, A.107, Q.108 Chain F: R.54, R.105, S.106, A.107, Q.108 Ligands: SO4.14 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:A.107, F:Q.108, E:A.107, E:Q.108 Salt bridges: F:R.54 SO4.20: 10 residues within 4Å: Chain G: R.54, R.105, S.106, A.107, Q.108 Chain H: R.54, S.106, A.107, Q.108 Ligands: SO4.23 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:A.107, G:Q.108, H:A.107, H:Q.108 Salt bridges: G:R.54 SO4.23: 10 residues within 4Å: Chain G: R.54, S.106, A.107, Q.108 Chain H: R.54, R.105, S.106, A.107, Q.108 Ligands: SO4.20 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:A.107, H:Q.108, G:A.107, G:Q.108 Salt bridges: H:R.54 SO4.26: 10 residues within 4Å: Chain I: R.54, R.105, S.106, A.107, Q.108 Chain J: R.54, S.106, A.107, Q.108 Ligands: SO4.29 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:A.107, I:Q.108, J:A.107, J:Q.108 Salt bridges: I:R.54 SO4.29: 10 residues within 4Å: Chain I: R.54, S.106, A.107, Q.108 Chain J: R.54, R.105, S.106, A.107, Q.108 Ligands: SO4.26 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:A.107, J:Q.108, I:A.107, I:Q.108 Salt bridges: J:R.54 SO4.32: 10 residues within 4Å: Chain K: R.54, R.105, S.106, A.107, Q.108 Chain L: R.54, S.106, A.107, Q.108 Ligands: SO4.35 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain K Hydrogen bonds: L:A.107, L:Q.108, K:A.107, K:Q.108 Salt bridges: K:R.54 SO4.35: 10 residues within 4Å: Chain K: R.54, S.106, A.107, Q.108 Chain L: R.54, R.105, S.106, A.107, Q.108 Ligands: SO4.32 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:A.107, L:Q.108, K:A.107, K:Q.108 Salt bridges: L:R.54

12 x 1JP: D-gamma-glutamyl-(Z)-N-(carboxymethylidene)-S-[(2R)-2-hydroxy-4-phenylbutyl]-L-cysteinamide(Non-covalent)

1JP.3: 18 residues within 4Å: Chain A: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 Chain J: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: A:Y.65, A:L.121, A:L.121, A:W.122, A:W.122, A:V.125, J:V.22, J:A.26 Hydrogen bonds: A:N.61, A:Y.65, J:S.29 Salt bridges: A:R.110, J:R.36 1JP.6: 18 residues within 4Å: Chain B: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 Chain L: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain L Hydrophobic interactions: B:Y.65, B:L.121, B:L.121, B:W.122, B:W.122, B:V.125, L:V.22, L:A.26 Hydrogen bonds: B:N.61, B:Y.65, L:S.29 Salt bridges: B:R.110, L:R.36 1JP.9: 18 residues within 4Å: Chain C: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 Chain K: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain K Hydrophobic interactions: C:Y.65, C:L.121, C:L.121, C:W.122, C:W.122, C:V.125, K:V.22, K:A.26 Hydrogen bonds: C:N.61, C:Y.99, K:S.29 Salt bridges: C:R.110, K:R.36 1JP.12: 18 residues within 4Å: Chain D: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 Chain I: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 13 PLIP interactions: 4 interactions with chain I, 9 interactions with chain D Hydrophobic interactions: I:V.22, I:A.26, D:Y.65, D:L.121, D:L.121, D:W.122, D:W.122, D:V.125 Hydrogen bonds: I:S.29, D:N.61, D:Y.99 Salt bridges: I:R.36, D:R.110 1JP.15: 18 residues within 4Å: Chain B: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain E: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain E Hydrophobic interactions: B:V.22, B:A.26, E:Y.65, E:L.121, E:L.121, E:W.122, E:W.122, E:V.125 Hydrogen bonds: B:S.29, E:N.61, E:Y.65 Salt bridges: B:R.36, E:R.110 1JP.18: 18 residues within 4Å: Chain D: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain F: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 9 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: F:Y.65, F:L.121, F:L.121, F:W.122, F:W.122, F:V.125, D:V.22, D:A.26 Hydrogen bonds: F:N.61, F:Y.99, D:S.29 Salt bridges: F:R.110, D:R.36 1JP.21: 18 residues within 4Å: Chain C: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain G: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain G Hydrophobic interactions: C:V.22, C:A.26, G:Y.65, G:L.121, G:L.121, G:W.122, G:W.122, G:V.125 Hydrogen bonds: C:S.29, G:N.61, G:Y.99 Salt bridges: C:R.36, G:R.110 1JP.24: 18 residues within 4Å: Chain A: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain H: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 9 interactions with chain H, 4 interactions with chain A Hydrophobic interactions: H:Y.65, H:L.121, H:L.121, H:W.122, H:W.122, H:V.125, A:V.22, A:A.26 Hydrogen bonds: H:N.61, H:Y.65, A:S.29 Salt bridges: H:R.110, A:R.36 1JP.27: 18 residues within 4Å: Chain F: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain I: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 9 interactions with chain I, 4 interactions with chain F Hydrophobic interactions: I:Y.65, I:L.121, I:L.121, I:W.122, I:W.122, I:V.125, F:V.22, F:A.26 Hydrogen bonds: I:N.61, I:Y.65, F:S.29 Salt bridges: I:R.110, F:R.36 1JP.30: 18 residues within 4Å: Chain H: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain J: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 9 interactions with chain J, 4 interactions with chain H Hydrophobic interactions: J:Y.65, J:L.121, J:L.121, J:W.122, J:W.122, J:V.125, H:V.22, H:A.26 Hydrogen bonds: J:N.61, J:Y.99, H:S.29 Salt bridges: J:R.110, H:R.36 1JP.33: 18 residues within 4Å: Chain G: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain K: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 4 interactions with chain G, 9 interactions with chain K Hydrophobic interactions: G:V.22, G:A.26, K:Y.65, K:L.121, K:L.121, K:W.122, K:W.122, K:V.125 Hydrogen bonds: G:S.29, K:N.61, K:Y.65 Salt bridges: G:R.36, K:R.110 1JP.36: 18 residues within 4Å: Chain E: V.22, A.26, S.29, L.30, V.32, I.33, R.36, Y.56, Q.59 Chain L: N.61, E.64, Y.65, Y.99, R.110, L.114, L.121, W.122, V.125 13 PLIP interactions: 4 interactions with chain E, 9 interactions with chain L Hydrophobic interactions: E:V.22, E:A.26, L:Y.65, L:L.121, L:L.121, L:W.122, L:W.122, L:V.125 Hydrogen bonds: E:S.29, L:N.61, L:Y.99 Salt bridges: E:R.36, L:R.110

Links

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Citation

Niegowski, D. et al., Crystal Structures of Leukotriene C4 Synthase in Complex with Product Analogs: IMPLICATIONS FOR THE ENZYME MECHANISM. J.Biol.Chem. (2014)

Release Date

2014-01-01

Peptides

Leukotriene C4 synthase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Leukotriene C4 synthase

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